[ { "name": "SC_RNA_COUNTER_CS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "recovered_cells", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_probes", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_target_umi_filter", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "force_cells", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "check_library_compatibility", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "auto", "id": "chemistry", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeting_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligner", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_polya_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_tso_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "emptydrops_minimum_umis", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "global_minimum_umis", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "max_mito_percent", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_ab_aggregate_detection", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 3, "id": "min_crispr_umi_threshold", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tenx_cloud_token_path", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_model", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "skip_cell_annotation", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/web_summary.html", "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_csv.csv", "id": "metrics_summary", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam", "id": "possorted_genome_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam.bai", "id": "possorted_genome_bai_index", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "possorted_genome_csi_index", "type": "bam.csi", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_mex", "id": "filtered_feature_bc_matrix", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_bc_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "id": "raw_feature_bc_matrix", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_feature_bc_matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis_csv", "id": "analysis", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "crispr_analysis", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.GET_AGGREGATE_BARCODES_OUT", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/chnk0-u3049cfb161/files/cloupe.cloupe", "id": "cloupe", "type": "cloupe", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/feature_reference.csv", "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types", "type": "CellTypes", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "web_summary_cell_types", "type": "html", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.GET_AGGREGATE_BARCODES_OUT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CELLRANGER_PREFLIGHT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/common/cellranger_preflight", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "auto", "id": "chemistry", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "full_check", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "recovered_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "force_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeting_method", "type": "string", "waiting": false } ], "Return": null }, "chunks": [ { "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [], "stagecodeLang": "Python", "type": "stage" }, { "name": "CELLRANGER_PREFLIGHT_LOCAL", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT_LOCAL", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT_LOCAL", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT_LOCAL", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/common/cellranger_preflight", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT_LOCAL/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT_LOCAL/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT_LOCAL/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "auto", "id": "chemistry", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "full_check", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "recovered_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "force_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeting_method", "type": "string", "waiting": false } ], "Return": null }, "chunks": [ { "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELLRANGER_PREFLIGHT_LOCAL/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [], "stagecodeLang": "Python", "type": "stage" }, { "name": "CELL_ANNOTATION_PREFLIGHT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.CELL_ANNOTATION_PREFLIGHT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELL_ANNOTATION_PREFLIGHT", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELL_ANNOTATION_PREFLIGHT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/cell_annotation_preflight", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELL_ANNOTATION_PREFLIGHT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELL_ANNOTATION_PREFLIGHT/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELL_ANNOTATION_PREFLIGHT/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_cr_annotate", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tenx_cloud_token_path", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_model", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "skip_cell_annotation", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cas_track_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cr_annotate_filtered_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cr_annotate_sample_cloupe", "type": "cloupe", "waiting": false } ], "Return": null }, "chunks": [ { "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/CELL_ANNOTATION_PREFLIGHT/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [], "stagecodeLang": "Python", "type": "stage" }, { "name": "COPY_CHEMISTRY_SPEC", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/COPY_CHEMISTRY_SPEC", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/COPY_CHEMISTRY_SPEC", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian copy_chemistry_spec", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/COPY_CHEMISTRY_SPEC/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/COPY_CHEMISTRY_SPEC/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/COPY_CHEMISTRY_SPEC/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_defs", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "auto", "id": "chemistry_spec", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC", "matchedFork": null, "value": { "Gene Expression": "auto" }, "id": "chemistry_specs", "type": "map\u003cstring\u003e", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/COPY_CHEMISTRY_SPEC/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FULL_COUNT_INPUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC", "matchedFork": null, "value": { "cell_annotation_model": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "chemistry_specs": { "Gene Expression": "auto" }, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "include_introns": true, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_secondary_analysis": false, "no_target_umi_filter": false, "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "skip_cell_annotation": true, "target_set": null, "target_set_name": null, "targeting_method": null, "tenx_cloud_token_path": null, "tenx_cmos": null }, "id": "cs_inputs", "type": "CountInputsMinimal", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ "auto", "custom", "threeprime", "fiveprime", "SC3Pv1", "SC3Pv2", "SC3Pv3-polyA", "SC3Pv3-CS1", "SC3Pv3LT", "SC3Pv3HT-polyA", "SC3Pv3HT-CS1", "SC3Pv4-polyA", "SC3Pv4-CS1", "SC5P-PE", "SC5P-PE-v3", "SC5P-R2", "SC5P-R2-v3", "SC5PHT", "SC-FB", "ARC-v1" ], "id": "allowed_chems", "type": "string[]", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC", "matchedFork": null, "value": { "Gene Expression": "auto" }, "id": "chemistry_specs", "type": "map\u003cstring\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "custom_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "id": "gene_index", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "name": "P5", "seq": "AATGATACGGCGACCACCGAGATCT" }, { "name": "P7", "seq": "CAAGCAGAAGACGGCATACGAGAT" }, { "name": "R1", "seq": "ACACTCTTTCCCTACACGACG" }, { "name": "R2", "seq": "GTGACTGGAGTTCAGACGTGTG" }, { "name": "switch_oligo", "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG" }, { "name": "polyA", "seq": "AAAAAAAAAAAAAAAAAAAA" } ], "id": "primers", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "id": "cell_calling_config", "type": "CellCalling", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_reads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "primer_initial_reads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "special_genomic_regions", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_polya_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_tso_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_probes", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_target_umi_filter", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_exons", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "skip_cell_annotation", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeting_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligner", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "genetic_demux_params", "type": "map", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "check_library_compatibility", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ "auto", "custom", "threeprime", "fiveprime", "SC3Pv1", "SC3Pv2", "SC3Pv3-polyA", "SC3Pv3-CS1", "SC3Pv3LT", "SC3Pv3HT-polyA", "SC3Pv3HT-CS1", "SC3Pv4-polyA", "SC3Pv4-CS1", "SC5P-PE", "SC5P-PE-v3", "SC5P-R2", "SC5P-R2-v3", "SC5PHT", "SC-FB", "ARC-v1" ], "id": "count_allowed_chems", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "throughput", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "id": "force_sample_barcodes", "type": "BarcodeAssignments", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tenx_cmos", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_assignment_confidence", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 3, "id": "min_crispr_umi_threshold", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "annotations", "type": "csv[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_model", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tenx_cloud_token_path", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "enable_tsne", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "WRITE_GENE_INDEX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_gene_index", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 6, "__vmem_gb": 9 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "id": "gene_index", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "GET_AGGREGATE_BARCODES_OUT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.GET_AGGREGATE_BARCODES_OUT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/GET_AGGREGATE_BARCODES_OUT", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/GET_AGGREGATE_BARCODES_OUT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/counter/get_aggregate_barcodes_out", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/GET_AGGREGATE_BARCODES_OUT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/GET_AGGREGATE_BARCODES_OUT/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/GET_AGGREGATE_BARCODES_OUT/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.GET_AGGREGATE_BARCODES_OUT", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/GET_AGGREGATE_BARCODES_OUT/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.GET_AGGREGATE_BARCODES_OUT" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SC_MULTI_CORE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "aligner": null, "annotations": null, "cell_annotation_model": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "chemistry_specs": { "Gene Expression": "auto" }, "custom_chemistry_def": null, "enable_tsne": true, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "genetic_demux_params": null, "include_exons": true, "include_introns": true, "initial_reads": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_secondary_analysis": false, "no_target_umi_filter": false, "primer_initial_reads": null, "primers": [ { "name": "P5", "seq": "AATGATACGGCGACCACCGAGATCT" }, { "name": "P7", "seq": "CAAGCAGAAGACGGCATACGAGAT" }, { "name": "R1", "seq": "ACACTCTTTCCCTACACGACG" }, { "name": "R2", "seq": "GTGACTGGAGTTCAGACGTGTG" }, { "name": "switch_oligo", "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG" }, { "name": "polyA", "seq": "AAAAAAAAAAAAAAAAAAAA" } ], "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "skip_cell_annotation": true, "special_genomic_regions": null, "subsample_rate": null, "target_set": null, "target_set_name": null, "targeting_method": null, "tenx_cloud_token_path": null, "tenx_cmos": null, "throughput": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "count_input", "type": "CountInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [], "id": "vdj_inputs", "type": "VdjInputs[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "disable_annotate": true, "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_rtl": true, "disable_vdj": true }, "id": "basic_config", "type": "BasicPipelineConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ "auto", "custom", "threeprime", "fiveprime", "SC3Pv1", "SC3Pv2", "SC3Pv3-polyA", "SC3Pv3-CS1", "SC3Pv3LT", "SC3Pv3HT-polyA", "SC3Pv3HT-CS1", "SC3Pv4-polyA", "SC3Pv4-CS1", "SC5P-PE", "SC5P-PE-v3", "SC5P-R2", "SC5P-R2-v3", "SC5PHT", "SC-FB", "ARC-v1" ], "id": "count_allowed_chems", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_RNA_COUNTER_CS", "id": "count_pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_allowed_chems", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_preflight", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_vdj_b": true, "disable_vdj_t": true, "disable_vdj_t_gd": true, "has_no_vdj_ref": true }, "id": "full_config", "type": "FullPipelineConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "split_vdj", "type": "SPLIT_VDJ_INPUTS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "count": { "basic_counter_outs": { "aggregate_barcodes": null, "alignments": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "annotation_files": null, "assign_tags": null, "bam_header": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "barcode_correction_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "barcode_counts": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "barcode_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "barcode_summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "bc_umi_info": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "counts_bc_order": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "filtered_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_mex", "gem_groups": [ 1 ], "gem_well_alignment_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json", "isotype_normalization_factors": null, "molecule_info": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "multi_matrices": null, "multi_metrics": null, "multi_molecule_info": null, "multi_pos_sorted_bam": null, "no_star_alignments": false, "nonambient_cell_calls": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/nonambient_calls.csv", "per_barcode_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "per_barcode_metrics_shard": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "per_probe_metrics": null, "per_read_gap_align": [], "possorted_genome_bai_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam.bai", "possorted_genome_bam": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam", "possorted_genome_csi_index": null, "raw_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "raw_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "raw_probe_bc_matrix": null, "read_chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "read_shards": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "sample_assignment_metrics": null, "sample_barcodes": null, "sequencing_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "slfe_feature_reference": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "target_set_name": null }, "setup_chunks_outs": { "barcode_whitelists": [ "3M-february-2018_TRU" ], "chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "visium_hd_slide_name": null }, "target_outs": { "bait_fasta": null, "disable_target_umi_filter": true, "disable_targeted": true, "no_bam": false, "probe_set": null, "target_gene_indices": null, "target_panel": null, "target_panel_or_probe_set": null, "target_panel_summary": null, "target_set_name": null, "targeting_method": null } }, "vdj_b": null, "vdj_filter_switch": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "vdj_t": null, "vdj_t_gd": null }, "id": "multi_gw", "type": "MULTI_GEM_WELL_PROCESSOR", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antibody_histograms": null, "antigen_histograms": null, "barcode_rank_plots": null, "cloupe": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/chnk0-u3049cfb161/files/cloupe.cloupe", "cmo_projection_plot": null, "count_summary": { "feature_reference": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/feature_reference.csv", "metrics_summary_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_csv.csv", "metrics_summary_json": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_json.json", "web_summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/web_summary.html", "ws_data": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/ws_data.json" }, "jibes_biplot_histogram": null }, "id": "multi_reporter", "type": "MULTI_REPORTER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "beam_analyzer", "type": "map\u003cBeamAnalyzerOutputs\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antibody_analyzer": null, "antigen_analyzer": null, "common_analyzer": { "analysis": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "analysis_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis_csv", "cloupe_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/cloupe_matrix_h5.h5", "skip_tsne": false, "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/summary.json" }, "crispr_analyzer": null, "targeted_analyzer": null }, "id": "count_analyzer", "type": "COUNT_ANALYZER", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "chemistry_defs": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "detected_probe_barcode_pairing": null, "is_antibody_only": false, "probe_barcode_overlap": null }, "id": "detect_count_chem", "type": "DETECT_CHEMISTRY", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": { "disable_antibody": true, "disable_antigen": true, "disable_crispr": true, "disable_gex": false, "disable_legacy_stages": false, "disable_library_cloupe": false, "disable_multiplexing": true, "disable_targeted": true }, "id": "disable_feat", "type": "DISABLE_FEATURE_STAGES", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_ref_out", "type": "VdjRefFolder", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_analyzer", "type": "map\u003cCOUNT_ANALYZER\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_reporter", "type": "map\u003cSAMPLE_REPORTER\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": {}, "id": "sample_outs", "type": "map\u003cSampleSlfeOuts\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-u3049cfab49/files/unassigned_alignments.bam", "id": "unassigned_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-u3049cfab49/files/unassigned_alignments_bai_index.bam.bai", "id": "unassigned_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-u3049cfab49/files/unassigned_alignments_csi_index.bam.csi", "id": "unassigned_csi", "type": "bam.csi", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_web_summary_json", "type": "WRITE_MULTI_WEB_SUMMARY_JSON", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_web_summaries", "type": "map\u003chtml\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_metrics_csvs", "type": "map\u003ccsv\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types", "type": "map\u003cCellTypes\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "library_cell_types", "type": "CellTypes", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COPY_VDJ_REFERENCE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.PICK_BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CELL_ANNOTATION_SERVICE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_positions", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_lowres_image", "type": "png", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "scale_factors", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_model", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tenx_cloud_token_path", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_LIBRARY", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "alert_string", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_projection", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_cloupe", "type": "cloupe", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types", "type": "CellTypes", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cas_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_cas_types", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_type_bar_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "spatial_cell_types_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_type_interactive_bar_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types_box_plot", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types_umap_plot", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "diffexp", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_cloupe_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_summarize", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.GENERATE_CAS_WEBSUMMARY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALL_CLOUD_CELL_TYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/CALL_CLOUD_CELL_TYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/CALL_CLOUD_CELL_TYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/call_cloud_cell_types", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/CALL_CLOUD_CELL_TYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/CALL_CLOUD_CELL_TYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/CALL_CLOUD_CELL_TYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "override_num_bc_limit", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_model", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tenx_cloud_token_path", "type": "file", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_LIBRARY", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_cloupe", "type": "cloupe", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_type_results", "type": "CellTypeResults", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_success", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "disable_cas_ws", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "disable_summarize", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "GENERATE_CAS_WEBSUMMARY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.GENERATE_CAS_WEBSUMMARY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/GENERATE_CAS_WEBSUMMARY", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/GENERATE_CAS_WEBSUMMARY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian generate_cas_websummary", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/GENERATE_CAS_WEBSUMMARY/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/GENERATE_CAS_WEBSUMMARY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/GENERATE_CAS_WEBSUMMARY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "alert_string", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_frac_returned_bcs", "type": "float", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_annotation_model", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_type_bar_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "diffexp", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "spatial_cell_types_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_type_interactive_bar_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types_box_plot", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types_umap_plot", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "metadata", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_success", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "disable_cas_ws", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_differential_expression", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_LIBRARY", "id": "pipestance_type", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "html", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_cloupe_name", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.GENERATE_CAS_WEBSUMMARY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.GENERATE_CAS_WEBSUMMARY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.GENERATE_CAS_WEBSUMMARY" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_CELL_TYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_type_results", "type": "CellTypeResults", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_positions", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_lowres_image", "type": "png", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "scale_factors", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_LIBRARY", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_success", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_projection", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cas_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_cas_types", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_type_bar_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "spatial_cell_types_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_type_interactive_bar_chart", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types_box_plot", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_types_umap_plot", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cas_diffexp_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "diffexp", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_differential_expression", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.ANALYZE_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.DISABLE_CAS_REPORTER_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BARCHART", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BOX_PLOT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_UMAP_PLOT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CLOUPE_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ANALYZE_CELL_TYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.ANALYZE_CELL_TYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/ANALYZE_CELL_TYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/ANALYZE_CELL_TYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/analyze_cell_types", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/ANALYZE_CELL_TYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/ANALYZE_CELL_TYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/ANALYZE_CELL_TYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_frac_returned_bcs", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_positions", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_lowres_image", "type": "png", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "scale_factors", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_model_used", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_LIBRARY", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_success", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "metadata", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.ANALYZE_CELL_TYPES", "matchedFork": null, "value": null, "id": "cas_metrics", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.ANALYZE_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_type_bar_chart", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.ANALYZE_CELL_TYPES", "matchedFork": null, "value": null, "id": "spatial_cell_types_chart", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.ANALYZE_CELL_TYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.ANALYZE_CELL_TYPES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "CELL_TYPE_DIFF_EXP", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrix", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "diffexp", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cas_diffexp_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.TIDY_CELLTYPE_DIFFEXP", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.DISABLE_CAS_REPORTER_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "DIFF_EXP_CAS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.DIFF_EXP_CAS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/DIFF_EXP_CAS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/DIFF_EXP_CAS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian diff_exp_stage", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/DIFF_EXP_CAS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/DIFF_EXP_CAS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/DIFF_EXP_CAS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5", "matchedFork": null, "value": null, "id": "clustering_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.DIFF_EXP_CAS", "matchedFork": null, "value": null, "id": "diffexp_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.DIFF_EXP_CAS", "matchedFork": null, "value": null, "id": "diffexp_csv", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.DIFF_EXP_CAS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.DIFF_EXP_CAS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "TIDY_CELLTYPE_DIFFEXP", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.TIDY_CELLTYPE_DIFFEXP", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/TIDY_CELLTYPE_DIFFEXP", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/TIDY_CELLTYPE_DIFFEXP", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/tidy_celltype_diffexp", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/TIDY_CELLTYPE_DIFFEXP/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/TIDY_CELLTYPE_DIFFEXP/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/TIDY_CELLTYPE_DIFFEXP/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.DIFF_EXP_CAS", "matchedFork": null, "value": null, "id": "diffexp_csv", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5", "matchedFork": null, "value": null, "id": "cell_types_map", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrix", "type": "h5", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.TIDY_CELLTYPE_DIFFEXP", "matchedFork": null, "value": null, "id": "cas_diffexp_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.TIDY_CELLTYPE_DIFFEXP", "matchedFork": null, "value": null, "id": "diffexp", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.DIFF_EXP_CAS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.TIDY_CELLTYPE_DIFFEXP" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.TIDY_CELLTYPE_DIFFEXP" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.TIDY_CELLTYPE_DIFFEXP" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_CELL_TYPES_H5", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/WRITE_CELL_TYPES_H5", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/WRITE_CELL_TYPES_H5", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/write_cell_types_h5", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/WRITE_CELL_TYPES_H5/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/WRITE_CELL_TYPES_H5/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/CELL_TYPE_DIFF_EXP/WRITE_CELL_TYPES_H5/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5", "matchedFork": null, "value": null, "id": "cell_types", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5", "matchedFork": null, "value": null, "id": "cell_types_map", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.CELL_TYPE_DIFF_EXP.WRITE_CELL_TYPES_H5" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "DISABLE_CAS_REPORTER_STAGES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.DISABLE_CAS_REPORTER_STAGES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/DISABLE_CAS_REPORTER_STAGES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/DISABLE_CAS_REPORTER_STAGES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/disable_cas_reporter_stages", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/DISABLE_CAS_REPORTER_STAGES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/DISABLE_CAS_REPORTER_STAGES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/DISABLE_CAS_REPORTER_STAGES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.DISABLE_CAS_REPORTER_STAGES", "matchedFork": null, "value": null, "id": "disable_differential_expression", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.DISABLE_CAS_REPORTER_STAGES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "GET_CELL_TYPES_BARCHART", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BARCHART", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BARCHART", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BARCHART", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/get_cell_types_barchart", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BARCHART/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BARCHART/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BARCHART/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BARCHART", "matchedFork": null, "value": null, "id": "cell_type_interactive_bar_chart", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BARCHART" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "GET_CELL_TYPES_BOX_PLOT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BOX_PLOT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BOX_PLOT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BOX_PLOT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/get_cell_types_box_plot", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BOX_PLOT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BOX_PLOT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_BOX_PLOT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_LIBRARY", "id": "pipestance_type", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BOX_PLOT", "matchedFork": null, "value": null, "id": "cell_types_box_plot", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BOX_PLOT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_BOX_PLOT" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "GET_CELL_TYPES_UMAP_PLOT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_UMAP_PLOT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_UMAP_PLOT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_UMAP_PLOT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/get_cell_types_umap_plot", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_UMAP_PLOT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_UMAP_PLOT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CELL_TYPES_UMAP_PLOT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_LIBRARY", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_projection", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_UMAP_PLOT", "matchedFork": null, "value": null, "id": "cell_types_umap_plot", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_UMAP_PLOT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CELL_TYPES_UMAP_PLOT" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "GET_CLOUPE_CELL_TYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CLOUPE_CELL_TYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CLOUPE_CELL_TYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CLOUPE_CELL_TYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/get_cloupe_cell_types", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CLOUPE_CELL_TYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CLOUPE_CELL_TYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_SERVICE/SUMMARIZE_CELL_TYPES/GET_CLOUPE_CELL_TYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "matchedFork": null, "value": null, "id": "cell_types", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CLOUPE_CELL_TYPES", "matchedFork": null, "value": null, "id": "cloupe_cas_types", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.CALL_CLOUD_CELL_TYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE.SUMMARIZE_CELL_TYPES.GET_CLOUPE_CELL_TYPES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/cell_annotation_viable_but_not_requested", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": null, "id": "filtered_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "skip_cell_annotation", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED", "matchedFork": null, "value": null, "id": "cell_annotation_viable_but_not_requested", "type": "map\u003cbool\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COPY_VDJ_REFERENCE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COPY_VDJ_REFERENCE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian copy_vdj_reference", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COPY_VDJ_REFERENCE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COPY_VDJ_REFERENCE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "COUNT_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "matchedFork": null, "value": { "aligner": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "custom_chemistry_def": null, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "include_exons": true, "include_introns": true, "initial_reads": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_target_umi_filter": false, "primers": [ { "name": "P5", "seq": "AATGATACGGCGACCACCGAGATCT" }, { "name": "P7", "seq": "CAAGCAGAAGACGGCATACGAGAT" }, { "name": "R1", "seq": "ACACTCTTTCCCTACACGACG" }, { "name": "R2", "seq": "GTGACTGGAGTTCAGACGTGTG" }, { "name": "switch_oligo", "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG" }, { "name": "polyA", "seq": "AAAAAAAAAAAAAAAAAAAA" } ], "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "subsample_rate": null, "target_set": null, "target_set_name": null, "targeting_method": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "count_inputs", "type": "CounterInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "id": "counter_metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": false, "id": "disable_rna", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_crispr", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_antibody", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_antigen", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_targeted", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": { "bait_fasta": null, "disable_target_umi_filter": true, "disable_targeted": true, "no_bam": false, "probe_set": null, "target_gene_indices": null, "target_panel": null, "target_panel_or_probe_set": null, "target_panel_summary": null, "target_set_name": null, "targeting_method": null }, "id": "parse_target_features", "type": "PARSE_TARGET_FEATURES", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "enable_tsne", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "analysis": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "analysis_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis_csv", "cloupe_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/cloupe_matrix_h5.h5", "skip_tsne": false, "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/summary.json" }, "id": "common_analyzer", "type": "AnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "crispr_analyzer", "type": "_CRISPR_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analyzer", "type": "_ANTIBODY_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_analyzer", "type": "_ANTIBODY_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeted_analyzer", "type": "_TARGETED_ANALYZER", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "DISABLE_SECONDARY_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.DISABLE_SECONDARY_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/DISABLE_SECONDARY_ANALYSIS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/DISABLE_SECONDARY_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/common/disable_secondary_analysis", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/DISABLE_SECONDARY_ANALYSIS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/DISABLE_SECONDARY_ANALYSIS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/DISABLE_SECONDARY_ANALYSIS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_visium_hd_main_run", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrices_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.DISABLE_SECONDARY_ANALYSIS", "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/DISABLE_SECONDARY_ANALYSIS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.DISABLE_SECONDARY_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.DISABLE_SECONDARY_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SC_RNA_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "aggr_library_info": null, "cbc_alpha": null, "cbc_knn": null, "cbc_realign_panorama": null, "cbc_sigma": null, "chemistry_batch_correction": false, "enable_tsne": true, "exclude_genes": null, "filtered_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "force_cells": null, "graphclust_neighbors": null, "graphclust_resolution": null, "is_pd": false, "is_spatial": false, "is_visium_hd": false, "max_clusters": null, "molecule_info": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "neighbor_a": null, "neighbor_b": null, "no_secondary_analysis": false, "num_analysis_bcs": null, "num_pca_bcs": null, "num_pca_genes": null, "num_principal_comps": null, "random_seed": null, "skip_multigenome_analysis": false, "tsne_input_pcs": null, "tsne_max_dims": null, "tsne_max_iter": null, "tsne_mom_switch_iter": null, "tsne_perplexity": null, "tsne_stop_lying_iter": null, "tsne_theta": null, "umap_implementation": "original", "umap_input_pcs": null, "umap_max_dims": null, "umap_metric": null, "umap_min_dist": null, "umap_n_neighbors": null, "use_bcs": null, "use_genes": null }, "id": "analyzer_inputs", "type": "AnalyzerInputs", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "analysis": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "analysis_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis_csv", "cloupe_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/cloupe_matrix_h5.h5", "skip_tsne": false, "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/summary.json" }, "id": "common_analyzer", "type": "AnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analyzer", "type": "_ANTIBODY_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_analyzer", "type": "_ANTIBODY_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u3049cfb090/files/clustering_h5.h5", "id": "clustering_h5", "type": "h5", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.DISABLE_SECONDARY_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ANALYZER_PREFLIGHT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/ANALYZER_PREFLIGHT", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/ANALYZER_PREFLIGHT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/analyzer_preflight", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/ANALYZER_PREFLIGHT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/ANALYZER_PREFLIGHT/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/ANALYZER_PREFLIGHT/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.DISABLE_SECONDARY_ANALYSIS", "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "use_genes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exclude_genes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "use_bcs", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_analysis_bcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "random_seed", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_pca_bcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_pca_genes", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_principal_comps", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "chemistry_batch_correction", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_knn", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_alpha", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_sigma", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_realign_panorama", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "max_clusters", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "graphclust_neighbors", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "neighbor_a", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "neighbor_b", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tsne_perplexity", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tsne_input_pcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tsne_max_dims", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tsne_max_iter", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tsne_stop_lying_iter", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tsne_mom_switch_iter", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tsne_theta", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umap_n_neighbors", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umap_input_pcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umap_max_dims", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umap_min_dist", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umap_metric", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "force_cells", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "skip_multigenome_analysis", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "skip", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "disable_run_pca", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": true, "id": "disable_correct_chemistry_batch", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "skip_multigenome_analysis", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/ANALYZER_PREFLIGHT/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.DISABLE_SECONDARY_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COMBINE_CLUSTERING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/combine_clustering", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/join-u3049cfab56/files/kmeans_h5.h5", "id": "kmeans_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/join-u3049cfab56/files/kmeans_csv", "id": "kmeans_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/join-u3049cfab56/files/clusters_h5.h5", "id": "graphclust_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/join-u3049cfab56/files/clusters_csv", "id": "graphclust_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "hclust_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "hclust_csv", "type": "path", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u3049cfb090/files/clustering_h5.h5", "id": "clustering_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u3049cfb090/files/clustering_csv", "id": "clustering_csv", "type": "path", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_HIERARCHICAL_CLUSTERING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_KMEANS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "CORRECT_CHEMISTRY_BATCH", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CORRECT_CHEMISTRY_BATCH", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/CORRECT_CHEMISTRY_BATCH", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/CORRECT_CHEMISTRY_BATCH", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/correct_chemistry_batch", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/CORRECT_CHEMISTRY_BATCH/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/CORRECT_CHEMISTRY_BATCH/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/CORRECT_CHEMISTRY_BATCH/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "dimred_matrix", "type": "pickle", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "matrix_barcode_feature_info", "type": "pickle", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "library_info", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "library_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_knn", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_alpha", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_sigma", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cbc_realign_panorama", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "batch_score_before_correction", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "batch_score_after_correction", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligned_pca_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligned_pca_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligned_pca_map", "type": "map\u003cPcaOutputs\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CORRECT_CHEMISTRY_BATCH" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CORRECT_CHEMISTRY_BATCH" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "PREPROCESS_MATRIX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/preprocess_matrix", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3, "__vmem_gb": 6 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "random_seed", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "use_genes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exclude_genes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "use_bcs", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_bcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "force_cells", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_visium_hd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "get_peak_matrix", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "enable_tsne", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "skip", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "disable_run_pca", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": true, "id": "disable_correct_chemistry_batch", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "matchedFork": null, "value": false, "id": "skip_multigenome_analysis", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": true, "id": "skip_antibody_analysis", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": true, "id": "skip_antigen_analysis", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/cloupe_matrix_h5.h5", "id": "cloupe_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "preprocessed_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "is_multi_genome", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "skip", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "skip_tsne", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "disable_run_pca", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": true, "id": "disable_correct_chemistry_batch", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "skip_multigenome_analysis", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": true, "id": "disable_hierarchical_clustering", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.ANALYZER_PREFLIGHT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "RUN_BATCH_CORRECTION_PCA", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_pcs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_atac", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "dimred_matrix", "type": "pickle", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "matrix_barcode_feature_info", "type": "pickle", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "library_type", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.POST_PCA", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "PCA_PREP", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/PCA_PREP", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/PCA_PREP", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/pca_prep", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/PCA_PREP/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/PCA_PREP/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/PCA_PREP/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_atac", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "matchedFork": null, "value": null, "id": "mem_gb", "type": "float", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "matchedFork": null, "value": null, "id": "filt_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "matchedFork": null, "value": null, "id": "library_type", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "POST_PCA", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.POST_PCA", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/POST_PCA", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/POST_PCA", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/post_pca", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/POST_PCA/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/POST_PCA/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/POST_PCA/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "matchedFork": null, "value": null, "id": "filt_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.RUN_PCA2", "matchedFork": null, "value": null, "id": "dimred_matrix_npy", "type": "npy", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "matchedFork": null, "value": null, "id": "mem_gb", "type": "float", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.POST_PCA", "matchedFork": null, "value": null, "id": "dimred_matrix", "type": "pickle", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.POST_PCA", "matchedFork": null, "value": null, "id": "matrix_barcode_feature_info", "type": "pickle", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.POST_PCA" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.POST_PCA" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.RUN_PCA2", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.POST_PCA" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "RUN_PCA2", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.RUN_PCA2", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/RUN_PCA2", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/RUN_PCA2", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian pca2_stage", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/RUN_PCA2/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/RUN_PCA2/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_BATCH_CORRECTION_PCA/RUN_PCA2/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "matchedFork": null, "value": null, "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_pcs", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.RUN_PCA2", "matchedFork": null, "value": null, "id": "dimred_matrix", "type": "npy", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.PCA_PREP", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_BATCH_CORRECTION_PCA.RUN_PCA2" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_DIFFERENTIAL_EXPRESSION", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian diff_exp_stage", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u3049cfb090/files/clustering_h5.h5", "id": "clustering_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u3049cfb091/files/diffexp_h5.h5", "id": "diffexp_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u3049cfb091/files/diffexp_csv", "id": "diffexp_csv", "type": "path", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 1, "cluster_type": "kmeans_2_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_2_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_3_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_3_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 3, "cluster_type": "kmeans_3_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_4_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_4_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 3, "cluster_type": "kmeans_4_clusters", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 4, "cluster_type": "kmeans_4_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_5_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_5_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 3, "cluster_type": "kmeans_5_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 4, "cluster_type": "kmeans_5_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 5, "cluster_type": "kmeans_5_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_6_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_6_clusters", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 1 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 3, "cluster_type": "kmeans_6_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 4, "cluster_type": "kmeans_6_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 5, "cluster_type": "kmeans_6_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 6, "cluster_type": "kmeans_6_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_7_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_7_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 3, "cluster_type": "kmeans_7_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 4, "cluster_type": "kmeans_7_clusters", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 2 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 5, "cluster_type": "kmeans_7_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 6, "cluster_type": "kmeans_7_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 7, "cluster_type": "kmeans_7_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 3, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 4, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 5, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 3 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 6, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 7, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 8, "cluster_type": "kmeans_8_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 3, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 4, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 5, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 4 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 6, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 7, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 8, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 9, "cluster_type": "kmeans_9_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 3, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 4, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 5 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 5, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 6, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 7, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 8, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 9, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 10, "cluster_type": "kmeans_10_clusters", "feature_type": "Gene Expression" }, { "cluster_id": 1, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 2, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 6 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 3, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 4, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 5, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 6, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 7, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 8, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 9, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 10, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 7 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 11, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 12, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 13, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 14, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 15, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 16, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 17, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 18, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 8 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 19, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 20, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 21, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 22, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 23, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 24, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 25, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 26, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 9 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 27, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 28, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 29, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 30, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 31, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 32, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 33, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 34, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 10 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 35, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 36, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 37, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 38, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 39, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 40, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 41, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 42, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 11 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 43, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 44, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 45, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 46, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 47, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 48, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 49, "cluster_type": "graphclust", "feature_type": "Gene Expression" }, { "cluster_id": 50, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 12 }, { "chunkDef": { "__mem_gb": 7, "__threads": 1, "__vmem_gb": 10, "cluster_keys": [ { "cluster_id": 51, "cluster_type": "graphclust", "feature_type": "Gene Expression" } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 13 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_GRAPH_CLUSTERING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian graph_clustering_stage", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_h5.h5", "id": "pca_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_neighbors", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "neighbor_a", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "neighbor_b", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "input_pcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "resolution", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "random_seed", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 4, "id": "threads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "parallel_clustering", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/join-u3049cfab56/files/clusters_h5.h5", "id": "clusters_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/join-u3049cfab56/files/clusters_csv", "id": "clusters_csv", "type": "path", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "feature_type": "Gene Expression" }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_HIERARCHICAL_CLUSTERING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_HIERARCHICAL_CLUSTERING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_HIERARCHICAL_CLUSTERING", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_HIERARCHICAL_CLUSTERING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian hierarchical_clustering_stage", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_HIERARCHICAL_CLUSTERING/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_HIERARCHICAL_CLUSTERING/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_HIERARCHICAL_CLUSTERING/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_GRAPH_CLUSTERING/fork0/join-u3049cfab56/files/clusters_h5.h5", "id": "graph_clusters_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clusters_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clusters_csv", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_HIERARCHICAL_CLUSTERING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_GRAPH_CLUSTERING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_HIERARCHICAL_CLUSTERING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_KMEANS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_KMEANS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/run_kmeans", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_h5.h5", "id": "pca_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "random_seed", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "max_clusters", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_bcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_pcs", "type": "int", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/join-u3049cfab56/files/kmeans_h5.h5", "id": "kmeans_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/join-u3049cfab56/files/kmeans_csv", "id": "kmeans_csv", "type": "path", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 2, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 3, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 1 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 4, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk2", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 2 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 5, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk3", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 3 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 6, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk4", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 4 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 7, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk5", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 5 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 8, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk6", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 6 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 9, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk7", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 7 }, { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "library": "Gene Expression", "n_clusters": 10, "which_pca": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_KMEANS/fork0/chnk8", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 8 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_KMEANS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_KMEANS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "RUN_MULTIGENOME_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/run_multigenome_analysis", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "is_multi_genome", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u3049cfab53/files/multi_genome_csv", "id": "multi_genome_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u3049cfab53/files/multi_genome_json", "id": "multi_genome_json", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u3049cfab53/files/multi_genome_summary.json", "id": "multi_genome_summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "RUN_PCA", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian pca_stage", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_pca_genes", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "num_principal_comps", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "pca_map", "type": "map\u003cPcaOutputs\u003e", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_h5.h5", "id": "pca_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_csv", "id": "pca_csv", "type": "path", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "feature_type": "Gene Expression" }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CORRECT_CHEMISTRY_BATCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_TSNE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_TSNE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian run_tsne", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_h5.h5", "id": "pca_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "random_seed", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "perplexity", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "input_pcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "max_dims", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "max_iter", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "stop_lying_iter", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "mom_switch_iter", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "theta", "type": "float", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-u3049cfab56/files/tsne_h5.h5", "id": "tsne_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-u3049cfab56/files/tsne_csv", "id": "tsne_csv", "type": "path", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "feature_type": "Gene Expression", "tsne_dims": 2 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_TSNE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_TSNE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_UMAP", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_UMAP", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_ana martian umap_stage", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_h5.h5", "id": "pca_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "original", "id": "implementation", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "random_seed", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "n_neighbors", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "input_pcs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "max_dims", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_dist", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metric", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u3049cfab56/files/umap_h5.h5", "id": "umap_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u3049cfab56/files/umap_csv", "id": "umap_csv", "type": "path", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 4, "__threads": 5, "__vmem_gb": 32, "feature_type": "Gene Expression", "umap_dims": 2 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_UMAP" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_UMAP" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/analyzer/summarize_analysis", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/preprocessed_matrix_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_h5.h5", "id": "pca_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u3049cfb090/files/clustering_h5.h5", "id": "clustering_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u3049cfb091/files/diffexp_h5.h5", "id": "diffexp_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-u3049cfab56/files/tsne_h5.h5", "id": "tsne_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u3049cfab56/files/umap_h5.h5", "id": "umap_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_PCA/fork0/join-u3049cfab53/files/pca_csv", "id": "pca_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/COMBINE_CLUSTERING/fork0/chnk0-u3049cfb090/files/clustering_csv", "id": "clustering_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_DIFFERENTIAL_EXPRESSION/fork0/join-u3049cfb091/files/diffexp_csv", "id": "diffexp_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_TSNE/fork0/join-u3049cfab56/files/tsne_csv", "id": "tsne_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_UMAP/fork0/join-u3049cfab56/files/umap_csv", "id": "umap_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u3049cfab53/files/multi_genome_summary.json", "id": "multi_genome_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u3049cfab53/files/multi_genome_csv", "id": "multi_genome_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/RUN_MULTIGENOME_ANALYSIS/fork0/join-u3049cfab53/files/multi_genome_json", "id": "multi_genome_json", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "matchedFork": null, "value": false, "id": "is_multi_genome", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "chemistry_batch_correction", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "batch_score_before_correction", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "batch_score_after_correction", "type": "float", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis_csv", "id": "analysis_csv", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/summary.json", "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.COMBINE_CLUSTERING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.CORRECT_CHEMISTRY_BATCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_DIFFERENTIAL_EXPRESSION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_MULTIGENOME_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_PCA", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_TSNE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.RUN_UMAP", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.SUMMARIZE_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_ANTIBODY_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALL_ANTIBODIES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/call_antibodies", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUMMARIZE_ANTIBODY_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/summarize_antibody_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "is_antibody", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_ANTIGEN_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER.PREPROCESS_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALL_ANTIBODIES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/call_antibodies", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUMMARIZE_ANTIBODY_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/summarize_antibody_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_antibody", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER.SC_RNA_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_ANTIBODY_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALL_ANTIBODIES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/call_antibodies", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/CALL_ANTIBODIES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.CALL_ANTIBODIES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUMMARIZE_ANTIBODY_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/summarize_antibody_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIBODY_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "is_antibody", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIBODY_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_ANTIGEN_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALL_ANTIBODIES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/call_antibodies", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/CALL_ANTIBODIES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_antibody", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_histograms_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES", "matchedFork": null, "value": null, "id": "antibody_treemap_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.CALL_ANTIBODIES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUMMARIZE_ANTIBODY_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/summarize_antibody_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_ANTIGEN_ANALYZER/SUMMARIZE_ANTIBODY_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_antibody", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS", "matchedFork": null, "value": null, "id": "antibody_analysis", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._ANTIGEN_ANALYZER.SUMMARIZE_ANTIBODY_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_CRISPR_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 3, "id": "min_crispr_umi_threshold", "type": "int", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_protospacer", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "crispr_analysis_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "crispr_analysis", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALL_PROTOSPACERS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/CALL_PROTOSPACERS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/CALL_PROTOSPACERS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/call_protospacers", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/CALL_PROTOSPACERS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/CALL_PROTOSPACERS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/CALL_PROTOSPACERS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 3, "id": "min_crispr_umi_threshold", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_calls_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_calls_per_cell", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_call_metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "cells_per_protospacer", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_umi_thresholds_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_umi_thresholds_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUMMARIZE_CRISPR_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/SUMMARIZE_CRISPR_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/SUMMARIZE_CRISPR_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/summarize_crispr_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/SUMMARIZE_CRISPR_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/SUMMARIZE_CRISPR_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/SUMMARIZE_CRISPR_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_calls_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_calls_per_cell", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "cells_per_protospacer", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_umi_thresholds_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_umi_thresholds_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE", "matchedFork": null, "value": null, "id": "perturbation_efficiencies_by_feature", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET", "matchedFork": null, "value": null, "id": "perturbations_efficiencies_by_target", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE", "matchedFork": null, "value": null, "id": "perturbation_effects_by_feature", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET", "matchedFork": null, "value": null, "id": "perturbation_effects_by_target", "type": "path", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS", "matchedFork": null, "value": null, "id": "crispr_analysis", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.SUMMARIZE_CRISPR_ANALYSIS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_PERTURBATIONS_BY_FEATURE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_FEATURE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_FEATURE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/measure_perturbations", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_FEATURE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_FEATURE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_FEATURE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_calls_per_cell", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "by_feature", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "ignore_multiples", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE", "matchedFork": null, "value": null, "id": "perturbation_efficiencies", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE", "matchedFork": null, "value": null, "id": "perturbation_effects_path", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_FEATURE" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_PERTURBATIONS_BY_TARGET", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_TARGET", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_TARGET", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/measure_perturbations", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_TARGET/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_TARGET/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_CRISPR_ANALYZER/_PERTURBATIONS_BY_TARGET/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "matchedFork": null, "value": null, "id": "protospacer_calls_per_cell", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "by_feature", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "ignore_multiples", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET", "matchedFork": null, "value": null, "id": "perturbation_efficiencies", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET", "matchedFork": null, "value": null, "id": "perturbation_effects_path", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER.CALL_PROTOSPACERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._CRISPR_ANALYZER._PERTURBATIONS_BY_TARGET" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_TARGETED_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_gene_bc_matrices", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "id": "basic_counter_summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_visium_hd", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeted_analysis_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_feature_metrics_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.CALCULATE_TARGETED_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALCULATE_TARGETED_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.CALCULATE_TARGETED_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/CALCULATE_TARGETED_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/CALCULATE_TARGETED_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/targeted/calculate_targeted_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/CALCULATE_TARGETED_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/CALCULATE_TARGETED_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/CALCULATE_TARGETED_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_gene_bc_matrices", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "id": "basic_counter_summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.CALCULATE_TARGETED_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.CALCULATE_TARGETED_METRICS", "matchedFork": null, "value": null, "id": "per_feature_metrics_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.CALCULATE_TARGETED_METRICS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "DISABLE_TARGETED_STAGES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.DISABLE_TARGETED_STAGES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/DISABLE_TARGETED_STAGES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/DISABLE_TARGETED_STAGES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/targeted/disable_targeted_stages", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/DISABLE_TARGETED_STAGES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/DISABLE_TARGETED_STAGES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/DISABLE_TARGETED_STAGES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_visium_hd", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.DISABLE_TARGETED_STAGES", "matchedFork": null, "value": null, "id": "disable_targeted_gdna", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.DISABLE_TARGETED_STAGES", "matchedFork": null, "value": null, "id": "disable_sampling_stages", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.DISABLE_TARGETED_STAGES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/MERGE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/MERGE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/MERGE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/MERGE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.CALCULATE_TARGETED_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_OFF_TARGET_READS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_ON_TARGET_READS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSAMPLE_OFF_TARGET_READS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_OFF_TARGET_READS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_OFF_TARGET_READS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_OFF_TARGET_READS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/counter/subsample_reads", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_OFF_TARGET_READS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_OFF_TARGET_READS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_OFF_TARGET_READS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "offtarget", "id": "target_mode", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.DISABLE_TARGETED_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_OFF_TARGET_READS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_OFF_TARGET_READS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUBSAMPLE_ON_TARGET_READS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_ON_TARGET_READS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_ON_TARGET_READS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_ON_TARGET_READS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/counter/subsample_reads", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_ON_TARGET_READS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_ON_TARGET_READS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/SUBSAMPLE_ON_TARGET_READS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "ontarget", "id": "target_mode", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.DISABLE_TARGETED_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_ON_TARGET_READS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.SUBSAMPLE_ON_TARGET_READS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_RUN_GDNA_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gdna_summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER.DISABLE_TARGETED_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "GET_GDNA_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian get_gdna_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_METRICS", "matchedFork": null, "value": null, "id": "gdna_plot_sufficient_stats", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "GET_GDNA_PLOT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_PLOT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_PLOT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_PLOT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/targeted/get_gdna_plot", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_PLOT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_PLOT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/GET_GDNA_PLOT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_METRICS", "matchedFork": null, "value": null, "id": "gdna_plot_sufficient_stats", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_PLOT", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_PLOT" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/MERGE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/MERGE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/MERGE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/_TARGETED_ANALYZER/_RUN_GDNA_ANALYSIS/MERGE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ null, null ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.GET_GDNA_PLOT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER._TARGETED_ANALYZER._RUN_GDNA_ANALYSIS.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CREATE_MULTI_GRAPH", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CREATE_MULTI_GRAPH", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CREATE_MULTI_GRAPH", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian create_multi_graph", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CREATE_MULTI_GRAPH/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CREATE_MULTI_GRAPH/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/CREATE_MULTI_GRAPH/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": null, "id": "detected_probe_barcode_pairing", "type": "json", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "DISABLE_FEATURE_STAGES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_FEATURE_STAGES", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_FEATURE_STAGES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/common/disable_feature_stages", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_FEATURE_STAGES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_FEATURE_STAGES/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_FEATURE_STAGES/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "disable_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_count", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "in_disable_targeted", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": {}, "id": "sample_outs", "type": "map\u003cSampleSlfeOuts\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_crispr", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_antibody", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_antigen", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_multiplexing", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_targeted", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": false, "id": "disable_legacy_stages", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": false, "id": "disable_library_cloupe", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": false, "id": "disable_gex", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_FEATURE_STAGES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "DISABLE_MULTI_CORE_STAGES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_MULTI_CORE_STAGES", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_MULTI_CORE_STAGES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/disable_multi_core_stages", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_MULTI_CORE_STAGES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_MULTI_CORE_STAGES/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_MULTI_CORE_STAGES/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_count", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "disable_multi_count", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": false, "id": "disable_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "skip_cell_annotation", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES", "matchedFork": null, "value": true, "id": "disable_sample_cas_celltyping", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES", "matchedFork": null, "value": true, "id": "disable_library_cas_celltyping", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/DISABLE_MULTI_CORE_STAGES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MAKE_FULL_CONFIG", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_input", "type": "VdjInputsCS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd_input", "type": "VdjInputsCS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b_input", "type": "VdjInputsCS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "disable_annotate": true, "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_rtl": true, "disable_vdj": true }, "id": "basic_config", "type": "BasicPipelineConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_vdj_b": true, "disable_vdj_t": true, "disable_vdj_t_gd": true, "has_no_vdj_ref": true }, "id": "config", "type": "FullPipelineConfig", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "_MAKE_VDJ_CONFIG", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/_MAKE_VDJ_CONFIG", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/_MAKE_VDJ_CONFIG", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/common/make_vdj_config", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/_MAKE_VDJ_CONFIG/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/_MAKE_VDJ_CONFIG/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/_MAKE_VDJ_CONFIG/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_input", "type": "VdjInputsCS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd_input", "type": "VdjInputsCS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b_input", "type": "VdjInputsCS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "disable_vdj", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "matchedFork": null, "value": true, "id": "disable_vdj_b", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "matchedFork": null, "value": true, "id": "disable_vdj_t", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "matchedFork": null, "value": true, "id": "disable_vdj_t_gd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "matchedFork": null, "value": true, "id": "has_no_vdj_ref", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MAKE_FULL_CONFIG/_MAKE_VDJ_CONFIG/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MULTI_CHEMISTRY_DETECTOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC", "matchedFork": null, "value": { "check_library_compatibility": true, "chemistry_specs": { "Gene Expression": "auto" }, "custom_chemistry_def": null, "feature_reference": null, "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ] }, "id": "count_inputs", "type": "CountChemistryInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [], "id": "vdj_inputs", "type": "VdjChemistryInputs[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "disable_annotate": true, "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_rtl": true, "disable_vdj": true }, "id": "basic_config", "type": "BasicPipelineConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ "auto", "custom", "threeprime", "fiveprime", "SC3Pv1", "SC3Pv2", "SC3Pv3-polyA", "SC3Pv3-CS1", "SC3Pv3LT", "SC3Pv3HT-polyA", "SC3Pv3HT-CS1", "SC3Pv4-polyA", "SC3Pv4-CS1", "SC5P-PE", "SC5P-PE-v3", "SC5P-R2", "SC5P-R2-v3", "SC5PHT", "SC-FB", "ARC-v1" ], "id": "count_allowed_chems", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_allowed_chems", "type": "string[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_defs_count", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "chemistry_defs": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "detected_probe_barcode_pairing": null, "is_antibody_only": false, "probe_barcode_overlap": null }, "id": "detect_count_chem", "type": "DETECT_CHEMISTRY", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "detect_vdj_chem", "type": "VDJ_CHEMISTRY_DETECTOR[]", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_SINGLE_BEAM_MODE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.VDJ_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CHECK_BARCODES_COMPATIBILITY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_BARCODES_COMPATIBILITY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_BARCODES_COMPATIBILITY", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_BARCODES_COMPATIBILITY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian check_barcodes_compatibility", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_BARCODES_COMPATIBILITY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_BARCODES_COMPATIBILITY/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_BARCODES_COMPATIBILITY/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "check_library_compatibility", "type": "bool", "waiting": false } ], "Return": null }, "chunks": [ { "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_BARCODES_COMPATIBILITY/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_BARCODES_COMPATIBILITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_BARCODES_COMPATIBILITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_BARCODES_COMPATIBILITY" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CHECK_SINGLE_BEAM_MODE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_SINGLE_BEAM_MODE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_SINGLE_BEAM_MODE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_SINGLE_BEAM_MODE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian check_single_beam_mode", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_SINGLE_BEAM_MODE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_SINGLE_BEAM_MODE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/CHECK_SINGLE_BEAM_MODE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "beam_modes", "type": "string[]", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.VDJ_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_SINGLE_BEAM_MODE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.CHECK_SINGLE_BEAM_MODE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "DETECT_COUNT_CHEMISTRY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian detect_chemistry", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 20, "__vmem_gb": 23 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ "auto", "custom", "threeprime", "fiveprime", "SC3Pv1", "SC3Pv2", "SC3Pv3-polyA", "SC3Pv3-CS1", "SC3Pv3LT", "SC3Pv3HT-polyA", "SC3Pv3HT-CS1", "SC3Pv4-polyA", "SC3Pv4-CS1", "SC5P-PE", "SC5P-PE-v3", "SC5P-R2", "SC5P-R2-v3", "SC5PHT", "SC-FB", "ARC-v1" ], "id": "allowed_chems", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC", "matchedFork": null, "value": { "Gene Expression": "auto" }, "id": "chemistry_specs", "type": "map\u003cstring\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "custom_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": null, "id": "probe_barcode_overlap", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": null, "id": "detected_probe_barcode_pairing", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 20, "__threads": 1, "__vmem_gb": 23 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VDJ_CHEMISTRY_DETECTOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.VDJ_CHEMISTRY_DETECTOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/VDJ_CHEMISTRY_DETECTOR", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/VDJ_CHEMISTRY_DETECTOR", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/VDJ_CHEMISTRY_DETECTOR/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/VDJ_CHEMISTRY_DETECTOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/VDJ_CHEMISTRY_DETECTOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "call": "VDJ_CHEMISTRY_DETECTOR", "mode": "array", "split": [] }, "id": "vdj_chem_inputs", "type": "VdjChemistryInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "count_chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "gex_sample_def", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "check_library_compatibility", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_count", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_allowed_chems", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config", "type": "csv", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.VDJ_CHEMISTRY_DETECTOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.VDJ_CHEMISTRY_DETECTOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.VDJ_CHEMISTRY_DETECTOR" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "MULTI_GEM_WELL_PROCESSOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_group", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "matchedFork": null, "value": { "aligner": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "custom_chemistry_def": null, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "include_exons": true, "include_introns": true, "initial_reads": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_target_umi_filter": false, "primers": [ { "name": "P5", "seq": "AATGATACGGCGACCACCGAGATCT" }, { "name": "P7", "seq": "CAAGCAGAAGACGGCATACGAGAT" }, { "name": "R1", "seq": "ACACTCTTTCCCTACACGACG" }, { "name": "R2", "seq": "GTGACTGGAGTTCAGACGTGTG" }, { "name": "switch_oligo", "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG" }, { "name": "polyA", "seq": "AAAAAAAAAAAAAAAAAAAA" } ], "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "subsample_rate": null, "target_set": null, "target_set_name": null, "targeting_method": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "count_inputs", "type": "CounterInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "chemistry_defs": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "detected_probe_barcode_pairing": null, "is_antibody_only": false, "probe_barcode_overlap": null }, "id": "count_chem", "type": "DETECT_CHEMISTRY", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_chem_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_inputs", "type": "VdjAssemblerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd_chem_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd_receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd_inputs", "type": "VdjAssemblerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b_chem_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b_receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b_inputs", "type": "VdjAssemblerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_vdj_b": true, "disable_vdj_t": true, "disable_vdj_t_gd": true, "has_no_vdj_ref": true }, "id": "config", "type": "FullPipelineConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "basic_counter_outs": { "aggregate_barcodes": null, "alignments": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "annotation_files": null, "assign_tags": null, "bam_header": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "barcode_correction_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "barcode_counts": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "barcode_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "barcode_summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "bc_umi_info": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "counts_bc_order": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "filtered_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_mex", "gem_groups": [ 1 ], "gem_well_alignment_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json", "isotype_normalization_factors": null, "molecule_info": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "multi_matrices": null, "multi_metrics": null, "multi_molecule_info": null, "multi_pos_sorted_bam": null, "no_star_alignments": false, "nonambient_cell_calls": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/nonambient_calls.csv", "per_barcode_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "per_barcode_metrics_shard": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "per_probe_metrics": null, "per_read_gap_align": [], "possorted_genome_bai_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam.bai", "possorted_genome_bam": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam", "possorted_genome_csi_index": null, "raw_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "raw_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "raw_probe_bc_matrix": null, "read_chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "read_shards": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "sample_assignment_metrics": null, "sample_barcodes": null, "sequencing_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "slfe_feature_reference": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "target_set_name": null }, "setup_chunks_outs": { "barcode_whitelists": [ "3M-february-2018_TRU" ], "chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "visium_hd_slide_name": null }, "target_outs": { "bait_fasta": null, "disable_target_umi_filter": true, "disable_targeted": true, "no_bam": false, "probe_set": null, "target_gene_indices": null, "target_panel": null, "target_panel_or_probe_set": null, "target_panel_summary": null, "target_set_name": null, "targeting_method": null } }, "id": "count", "type": "COUNT_GEM_WELL_PROCESSOR", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t", "type": "VDJ_GEM_WELL_PROCESSOR", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd", "type": "VDJ_GEM_WELL_PROCESSOR", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b", "type": "VDJ_GEM_WELL_PROCESSOR", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "vdj_filter_switch", "type": "FilterSwitch", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "COUNT_GEM_WELL_PROCESSOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_group", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "matchedFork": null, "value": { "aligner": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "custom_chemistry_def": null, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "include_exons": true, "include_introns": true, "initial_reads": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_target_umi_filter": false, "primers": [ { "name": "P5", "seq": "AATGATACGGCGACCACCGAGATCT" }, { "name": "P7", "seq": "CAAGCAGAAGACGGCATACGAGAT" }, { "name": "R1", "seq": "ACACTCTTTCCCTACACGACG" }, { "name": "R2", "seq": "GTGACTGGAGTTCAGACGTGTG" }, { "name": "switch_oligo", "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG" }, { "name": "polyA", "seq": "AAAAAAAAAAAAAAAAAAAA" } ], "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "subsample_rate": null, "target_set": null, "target_set_name": null, "targeting_method": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "inputs", "type": "CounterInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "chemistry_defs": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "detected_probe_barcode_pairing": null, "is_antibody_only": false, "probe_barcode_overlap": null }, "id": "chem", "type": "DETECT_CHEMISTRY", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "disable_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": { "bait_fasta": null, "disable_target_umi_filter": true, "disable_targeted": true, "no_bam": false, "probe_set": null, "target_gene_indices": null, "target_panel": null, "target_panel_or_probe_set": null, "target_panel_summary": null, "target_set_name": null, "targeting_method": null }, "id": "target_outs", "type": "PARSE_TARGET_FEATURES", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode_whitelists": [ "3M-february-2018_TRU" ], "chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "visium_hd_slide_name": null }, "id": "setup_chunks_outs", "type": "MULTI_SETUP_CHUNKS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "aggregate_barcodes": null, "alignments": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "annotation_files": null, "assign_tags": null, "bam_header": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "barcode_correction_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "barcode_counts": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "barcode_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "barcode_summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "bc_umi_info": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "counts_bc_order": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "filtered_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_mex", "gem_groups": [ 1 ], "gem_well_alignment_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json", "isotype_normalization_factors": null, "molecule_info": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "multi_matrices": null, "multi_metrics": null, "multi_molecule_info": null, "multi_pos_sorted_bam": null, "no_star_alignments": false, "nonambient_cell_calls": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/nonambient_calls.csv", "per_barcode_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "per_barcode_metrics_shard": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "per_probe_metrics": null, "per_read_gap_align": [], "possorted_genome_bai_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam.bai", "possorted_genome_bam": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam", "possorted_genome_csi_index": null, "raw_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "raw_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "raw_probe_bc_matrix": null, "read_chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "read_shards": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "sample_assignment_metrics": null, "sample_barcodes": null, "sequencing_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "slfe_feature_reference": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "target_set_name": null }, "id": "basic_counter_outs", "type": "_BASIC_SC_RNA_COUNTER", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "MULTI_SETUP_CHUNKS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian multi_setup_chunks", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "default_library_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "id": "sample_def", "type": "map[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ "3M-february-2018_TRU" ], "id": "barcode_whitelists", "type": "string[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "visium_hd_slide_name", "type": "string", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "PARSE_TARGET_FEATURES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/PARSE_TARGET_FEATURES", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/PARSE_TARGET_FEATURES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/common/parse_target_features", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/PARSE_TARGET_FEATURES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/PARSE_TARGET_FEATURES/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/PARSE_TARGET_FEATURES/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "id": "gene_index", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_probes", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_target_umi_filter", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "bait_fasta", "type": "fa", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_or_probe_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_gene_indices", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "disable_targeted", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "disable_target_umi_filter", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "targeting_method", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/PARSE_TARGET_FEATURES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_BASIC_SC_RNA_COUNTER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "disable_target_umi_filter", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_features", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "disable_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_probes", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "id": "cell_calling_config", "type": "CellCalling", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_reads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_polya_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_tso_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1000, "id": "min_reads_to_report_bc", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_exons", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligner", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "id": "force_sample_barcodes", "type": "BarcodeAssignments", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_assignment_confidence", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "slide_serial_capture_area", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "v1_pattern_fix", "type": "V1PatternFixArgs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_visium_hd", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/nonambient_calls.csv", "id": "nonambient_cell_calls", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "id": "barcode_correction_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "id": "bam_header", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam", "id": "possorted_genome_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam.bai", "id": "possorted_genome_bai_index", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "possorted_genome_csi_index", "type": "bam.csi", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "id": "barcode_counts", "type": "tbcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_gene_bc_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "id": "raw_gene_bc_matrices_mex", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_gene_bc_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_mex", "id": "filtered_gene_bc_matrices_mex", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "annotation_files", "type": "AnnotationFiles", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_probe_metrics", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "raw_probe_bc_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json", "id": "gem_well_alignment_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "assign_tags", "type": "AssignTagsOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_pos_sorted_bam", "type": "SampleBamFile[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_molecule_info", "type": "SampleMoleculeInfo[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_metrics", "type": "SampleMetrics[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_assignment_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "id": "per_barcode_metrics", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "isotype_normalization_factors", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_metrics_shard", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "id": "bc_umi_info", "type": "bui[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "id": "alignments", "type": "asf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "slfe_feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "id": "counts_bc_order", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": false, "id": "no_star_alignments", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [], "id": "per_read_gap_align", "type": "parquet[]", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.WRITE_POS_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CHECK_CORRECTION_FACTOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.CHECK_CORRECTION_FACTOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/CHECK_CORRECTION_FACTOR", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/CHECK_CORRECTION_FACTOR", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/spatial/check_correction_factor", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/CHECK_CORRECTION_FACTOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/CHECK_CORRECTION_FACTOR/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/CHECK_CORRECTION_FACTOR/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "v1_pattern_fix", "type": "V1PatternFixArgs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_fbm", "type": "h5", "waiting": false } ], "Return": null }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/CHECK_CORRECTION_FACTOR/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.CHECK_CORRECTION_FACTOR" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COLLATE_PROBE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/COLLATE_PROBE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/COLLATE_PROBE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian collate_probe_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/COLLATE_PROBE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/COLLATE_PROBE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/COLLATE_PROBE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "probe_barcode_counts", "type": "csf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set_name", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index_path", "type": "bi.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_probe_metrics", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "raw_probe_bc_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "estimated_gdna_metrics", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "DEMUX_PROBE_BC_MATRIX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DEMUX_PROBE_BC_MATRIX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DEMUX_PROBE_BC_MATRIX", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DEMUX_PROBE_BC_MATRIX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian demux_probe_bc_matrix", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DEMUX_PROBE_BC_MATRIX/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DEMUX_PROBE_BC_MATRIX/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DEMUX_PROBE_BC_MATRIX/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "probe_barcode_counts", "type": "csf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_cell_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_raw_probe_bc_matrices", "type": "map\u003ch5\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "samples_per_probe_metrics", "type": "map\u003ccsv\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DEMUX_PROBE_BC_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DEMUX_PROBE_BC_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DEMUX_PROBE_BC_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DEMUX_PROBE_BC_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DEMUX_PROBE_BC_MATRIX" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "DISABLE_STAGES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DISABLE_STAGES", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DISABLE_STAGES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/disable_stages", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DISABLE_STAGES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DISABLE_STAGES/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DISABLE_STAGES/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_feature_bc_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "probe_barcode_counts", "type": "csf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "disable_multi", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_visium_hd", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": false, "id": "disable_legacy_bam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": true, "id": "disable_sample_bams", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": true, "id": "disable_assign_tags", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": false, "id": "disable_subsampling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": true, "id": "no_probe_barcode_counts", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": true, "id": "no_probe_barcode_matrix_demux", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/DISABLE_STAGES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "FILTER_BARCODES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/counter/filter_barcodes", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "id": "barcode_correction_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "id": "config", "type": "CellCalling", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "id": "per_barcode_metrics", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_spatial", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_mex", "id": "filtered_matrices_mex", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/nonambient_calls.csv", "id": "nonambient_calls", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/mitochondrial_summary.csv", "id": "mitochondrial_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "isotype_normalization_factors", "type": "csv", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "probe_bc_def": null }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "INFER_GEM_WELL_THROUGHPUT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/INFER_GEM_WELL_THROUGHPUT", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/INFER_GEM_WELL_THROUGHPUT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/infer_gem_well_throughput", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/INFER_GEM_WELL_THROUGHPUT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/INFER_GEM_WELL_THROUGHPUT/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/INFER_GEM_WELL_THROUGHPUT/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "throughput", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "matchedFork": null, "value": null, "id": "throughput", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "matchedFork": null, "value": null, "id": "inferred_throughputs", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/INFER_GEM_WELL_THROUGHPUT/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u3049cfb089/files/summary.json", null, null ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTI_COLLATE_PER_SAMPLE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_COLLATE_PER_SAMPLE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_COLLATE_PER_SAMPLE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian collate_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_COLLATE_PER_SAMPLE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_COLLATE_PER_SAMPLE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_COLLATE_PER_SAMPLE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTI_WRITE_PER_SAMPLE_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_BAM", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_pos_bam", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_BAM/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_BAM/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_BAM/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "slide_serial_capture_area", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "id": "bam_header", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "id": "alignments", "type": "asf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "pos_sorted_bam", "type": "SampleBamFile", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_pos_sorted_bam", "type": "SampleBamFile[]", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTI_WRITE_PER_SAMPLE_MATRICES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MATRICES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MATRICES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/multi_write_per_sample_matrices", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MATRICES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_matrix_h5", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_raw_probe_bc_matrices", "type": "map\u003ch5\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "samples_per_probe_metrics", "type": "map\u003ccsv\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DEMUX_PROBE_BC_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MATRICES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_molecule_info", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "id": "counts_bc_order", "type": "bui[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3049cf9433/files/summary.json", "id": "matrix_computer_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "recovered_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "force_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_probe_metrics", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_probes", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_ab_aggregate_detection", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_high_occupancy_gem_detection", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_sample_metrics", "type": "SampleMetrics[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "slide_serial_capture_area", "type": "string", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_COLLATE_PER_SAMPLE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.MULTI_WRITE_PER_SAMPLE_MOLECULE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_POS_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.WRITE_POS_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_pos_bam", "forks": [ { "argPermute": null, "joinDef": { "__threads": 4, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "slide_serial_capture_area", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "id": "bam_header", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "id": "alignments", "type": "asf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "bai_index_file": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam.bai", "bam_file": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam", "csi_index_file": null, "sample": "non_multiplexed" }, "id": "pos_sorted_bam", "type": "SampleBamFile", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_pos_sorted_bam", "type": "SampleBamFile[]", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 11, 399746, false, 3038056539121740983, 1630384850, 0 ], "start": null }, "write_header": true }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 5355, 27736, false, 17512680646486377317, 728404078, 16 ], "start": [ 11, 399746, false, 3038056539121740983, 1630384850, 0 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 1 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 411147955214422209, 6346873, 4 ], "start": [ 5355, 27736, false, 17512680646486377317, 728404078, 16 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 2 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 1051384494836050238, 6346873, 4 ], "start": [ 4294967295, -1, true, 411147955214422209, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 3 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 1688881541692443892, 6346873, 4 ], "start": [ 4294967295, -1, true, 1051384494836050238, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 4 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 2333106137281241172, 6346873, 4 ], "start": [ 4294967295, -1, true, 1688881541692443892, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 5 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 2974259214567669100, 6346873, 4 ], "start": [ 4294967295, -1, true, 2333106137281241172, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 6 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 3614847038414737121, 6346873, 4 ], "start": [ 4294967295, -1, true, 2974259214567669100, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 7 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 4255202124386345324, 6346873, 4 ], "start": [ 4294967295, -1, true, 3614847038414737121, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 8 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 4896042050095282461, 6346873, 4 ], "start": [ 4294967295, -1, true, 4255202124386345324, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 9 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 5537247165389517980, 6346873, 4 ], "start": [ 4294967295, -1, true, 4896042050095282461, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 10 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 6174267776997847024, 6346873, 4 ], "start": [ 4294967295, -1, true, 5537247165389517980, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 11 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 6814249310915988543, 6346873, 4 ], "start": [ 4294967295, -1, true, 6174267776997847024, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 12 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 7452517212826741574, 6346873, 4 ], "start": [ 4294967295, -1, true, 6814249310915988543, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 13 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 8086196243498075819, 6346873, 4 ], "start": [ 4294967295, -1, true, 7452517212826741574, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 14 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 8722726461996762577, 6346873, 4 ], "start": [ 4294967295, -1, true, 8086196243498075819, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 15 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 9358883437884496770, 6346873, 4 ], "start": [ 4294967295, -1, true, 8722726461996762577, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 16 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 9996704601677608374, 6346873, 4 ], "start": [ 4294967295, -1, true, 9358883437884496770, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 17 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 10628724880557013434, 6346873, 4 ], "start": [ 4294967295, -1, true, 9996704601677608374, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 18 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 11262350376266638098, 6346873, 4 ], "start": [ 4294967295, -1, true, 10628724880557013434, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 19 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 11899029896105012579, 6346873, 4 ], "start": [ 4294967295, -1, true, 11262350376266638098, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 20 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 12529215165542668548, 6346873, 4 ], "start": [ 4294967295, -1, true, 11899029896105012579, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 21 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 13167274869511664714, 6346873, 4 ], "start": [ 4294967295, -1, true, 12529215165542668548, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 22 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 13817445275805915226, 6346873, 4 ], "start": [ 4294967295, -1, true, 13167274869511664714, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 23 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 14442387249958047182, 6346873, 4 ], "start": [ 4294967295, -1, true, 13817445275805915226, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 24 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 15116190930495158312, 6346873, 4 ], "start": [ 4294967295, -1, true, 14442387249958047182, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 25 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 15871974352925972139, 6346873, 4 ], "start": [ 4294967295, -1, true, 15116190930495158312, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 26 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 16391025096407076532, 6346873, 4 ], "start": [ 4294967295, -1, true, 15871974352925972139, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 27 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 17121833552064961208, 6346873, 4 ], "start": [ 4294967295, -1, true, 16391025096407076532, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 28 }, { "chunkDef": { "__mem_gb": 3, "__threads": 2, "__vmem_gb": 6, "range": { "end": [ 4294967295, -1, true, 17891428529557746074, 6346873, 4 ], "start": [ 4294967295, -1, true, 17121833552064961208, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 29 }, { "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": null, "start": [ 4294967295, -1, true, 17891428529557746074, 6346873, 4 ] }, "write_header": false }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/chnk30", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 30 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.WRITE_POS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.WRITE_POS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.WRITE_POS_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "_ASSIGN_TAGS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_feature_bc_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "id": "force_sample_barcodes", "type": "BarcodeAssignments", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_assignment_confidence", "type": "float", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "matchedFork": null, "value": null, "id": "throughput", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "matchedFork": null, "value": null, "id": "inferred_throughputs", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "assign_tags_outs", "type": "AssignTagsOuts", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_MARGINAL", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALL_TAGS_JIBES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_JIBES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_JIBES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/call_tags_jibes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_JIBES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_JIBES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_JIBES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "marginal_tag_calls_per_cell", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "marginal_tag_frequencies", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "matchedFork": null, "value": null, "id": "throughput", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_assignment_confidence", "type": "float", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "library_type", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "jibes_parameters", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "jibes_model_summary", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "jibes_summary_data", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "assignment_confidence_table", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_calls_summary", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_calls_per_cell", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_call_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_umi_thresholds_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_umi_thresholds_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_assigner_pickle", "type": "pickle", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "non_singlet_barcodes", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_MARGINAL", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "CALL_TAGS_MARGINAL", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_MARGINAL", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_MARGINAL", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_MARGINAL", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/call_tags_marginal", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_MARGINAL/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_MARGINAL/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_MARGINAL/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "matchedFork": null, "value": null, "id": "throughput", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "library_type", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "marginal_tag_calls_per_cell", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "marginal_tag_frequencies", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_contaminant_info", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_MARGINAL" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.INFER_GEM_WELL_THROUGHPUT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_MARGINAL" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_MARGINAL" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "CALL_TAGS_OH", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_OH", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_OH", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_OH", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian call_tags_oh", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_OH/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_OH/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_OH/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_feature_bc_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_bc_matrix", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_OH" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_OH" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_OH" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_OH" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CALL_TAGS_RTL", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_RTL", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_RTL", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian call_tags_rtl", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_RTL/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_RTL/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/CALL_TAGS_RTL/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_feature_bc_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_bc_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "frp_gem_barcode_overlap", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "COMPUTE_EXTRA_MULTIPLEXING_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/COMPUTE_EXTRA_MULTIPLEXING_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/COMPUTE_EXTRA_MULTIPLEXING_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/compute_extra_multiplexing_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/COMPUTE_EXTRA_MULTIPLEXING_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/COMPUTE_EXTRA_MULTIPLEXING_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/COMPUTE_EXTRA_MULTIPLEXING_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "sample_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "non_singlet_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "DETERMINE_SAMPLE_ASSIGNMENTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/DETERMINE_SAMPLE_ASSIGNMENTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/DETERMINE_SAMPLE_ASSIGNMENTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/determine_sample_assignments", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/DETERMINE_SAMPLE_ASSIGNMENTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/DETERMINE_SAMPLE_ASSIGNMENTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/DETERMINE_SAMPLE_ASSIGNMENTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null ], "id": "barcodes_per_tag", "type": "json[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "id": "force_sample_barcodes", "type": "BarcodeAssignments", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "non_singlet_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_feature_bc_matrix", "type": "h5", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "cells_per_tag", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "sample_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "non_singlet_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "sample_summaries", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_OH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MERGE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MERGE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MERGE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MERGE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_JIBES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_OH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.CALL_TAGS_RTL", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.COMPUTE_EXTRA_MULTIPLEXING_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.DETERMINE_SAMPLE_ASSIGNMENTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTIPLEXING_METHOD", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MULTIPLEXING_METHOD", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MULTIPLEXING_METHOD", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/multiplexing_method", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MULTIPLEXING_METHOD/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MULTIPLEXING_METHOD/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_ASSIGN_TAGS/MULTIPLEXING_METHOD/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "multiplexing_is_not_rtl", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "multiplexing_is_not_cmo_or_hashtag", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "multiplexing_is_not_oh", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "output_per_sample_raw_matrix", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._ASSIGN_TAGS.MULTIPLEXING_METHOD" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "_CELLS_REPORTER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "recovered_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "force_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_ab_aggregate_detection", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_high_occupancy_gem_detection", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "slfe_feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "id": "report_mol_inputs", "type": "bui[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3049cf9433/files/summary.json", "id": "matrix_computer_summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_probe_metrics", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/summary.json", "id": "filter_barcodes_summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "id": "per_barcode_metrics", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_probes", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": false, "id": "disable_subsampling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "slide_serial_capture_area", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u3049cfb089/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "SUBSAMPLE_READS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUBSAMPLE_READS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/counter/subsample_reads", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1.5, "__vmem_gb": 4.5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_mode", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u3049cfab49/files/summary.json", "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 3.1, "__threads": 1, "__vmem_gb": 12.3, "chunk_len": 103330, "chunk_start": 0, "subsample_info": [ { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 753, "library_subsample_rates": [ 0.09994601837377148 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 1000, "library_subsample_rates": [ 0.13273043608734594 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 1506, "library_subsample_rates": [ 0.19989203674754297 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 2260, "library_subsample_rates": [ 0.2999707855574018 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 3000, "library_subsample_rates": [ 0.3981913082620378 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 3013, "library_subsample_rates": [ 0.3999168039311733 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 3767, "library_subsample_rates": [ 0.49999555274103213 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 4520, "library_subsample_rates": [ 0.5999415711148036 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 5000, "library_subsample_rates": [ 0.6636521804367297 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 5273, "library_subsample_rates": [ 0.6998875894885751 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 6027, "library_subsample_rates": [ 0.7999663382984339 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 6780, "library_subsample_rates": [ 0.8999123566722056 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 7534, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 20000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 30000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 1, "library_subsample_rates": [ 0.050028173483894156 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 3, "library_subsample_rates": [ 0.15008452045168247 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 5, "library_subsample_rates": [ 0.2501408674194708 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 7, "library_subsample_rates": [ 0.3501972143872591 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 9, "library_subsample_rates": [ 0.4502535613550474 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 11, "library_subsample_rates": [ 0.5503099083228358 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 13, "library_subsample_rates": [ 0.6503662552906241 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 15, "library_subsample_rates": [ 0.7504226022584124 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 17, "library_subsample_rates": [ 0.8504789492262007 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 19, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 1000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 3000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 5000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 20000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 30000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 2.147915463829532e-05 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.00010739577319147661 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 100000, "library_subsample_rates": [ 0.00021479154638295322 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 250000, "library_subsample_rates": [ 0.0005369788659573831 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 500000, "library_subsample_rates": [ 0.0010739577319147662 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 1000000, "library_subsample_rates": [ 0.0021479154638295323 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 2500000, "library_subsample_rates": [ 0.00536978865957383 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 5000000, "library_subsample_rates": [ 0.01073957731914766 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 7500000, "library_subsample_rates": [ 0.01610936597872149 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 10000000, "library_subsample_rates": [ 0.02147915463829532 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 46556767, "library_subsample_rates": [ 0.09999999978520846 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 50000000, "library_subsample_rates": [ 0.1073957731914766 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 93113534, "library_subsample_rates": [ 0.19999999957041692 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 100000000, "library_subsample_rates": [ 0.2147915463829532 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 139670301, "library_subsample_rates": [ 0.2999999993556254 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 186227068, "library_subsample_rates": [ 0.39999999914083384 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 232783835, "library_subsample_rates": [ 0.49999999892604224 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 279340602, "library_subsample_rates": [ 0.5999999987112508 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 325897369, "library_subsample_rates": [ 0.6999999984964592 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 372454136, "library_subsample_rates": [ 0.7999999982816677 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 419010903, "library_subsample_rates": [ 0.899999998066876 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 465567671, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 1000000000, "library_subsample_rates": [ 0.0 ] } ] }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUBSAMPLE_READS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUBSAMPLE_READS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUBSAMPLE_READS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUMMARIZE_BASIC_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/counter/summarize_basic_reports", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 7, "__vmem_gb": 10 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "id": "per_barcode_metrics", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3049cf9433/files/summary.json", "id": "matrix_computer_summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "recovered_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "sample_bcs_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3049cf9433/files/summary.json", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u3049cfab49/files/summary.json", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/non_multiplexed_summary.json", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/summary.json" ], "id": "summary_jsons", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u3049cfb089/files/summary.json", "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUBSAMPLE_READS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_MOLECULE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_molecule_info", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 12, "__vmem_gb": 15 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "id": "counts_bc_order", "type": "bui[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3049cf9433/files/summary.json", "id": "matrix_computer_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "recovered_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "per_gem_well": null, "per_sample": null }, "id": "force_cells", "type": "CellCallingParam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_probe_metrics", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_probes", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_ab_aggregate_detection", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_high_occupancy_gem_detection", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_sample_metrics", "type": "SampleMetrics[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "slide_serial_capture_area", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": { "h5_file": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "sample": "non_multiplexed", "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/non_multiplexed_summary.json" }, "id": "single_mol_info", "type": "SampleMoleculeInfo", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": null, "id": "multi_mol_info", "type": "SampleMoleculeInfo[]", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.COLLATE_PROBE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.WRITE_MOLECULE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "_MATRIX_COMPUTER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_under_tissue", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_reads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_polya_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_tso_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1000, "id": "min_reads_to_report_bc", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_features", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_exons", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligner", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "disable_target_umi_filter", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "v1_pattern_fix", "type": "V1PatternFixArgs", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "slfe_feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "id": "barcode_correction_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "raw_gene_bc_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "id": "raw_gene_bc_matrices_mex", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "id": "counts_bc_order", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "id": "report_mol_inputs", "type": "bui[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3049cf9433/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "annotation_files", "type": "AnnotationFiles", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "id": "per_barcode_metrics", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_metrics_shard", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "id": "bc_umi_info", "type": "bui[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "probe_barcode_counts", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "id": "bam_header", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "id": "alignments", "type": "asf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": null, "id": "multi_metrics", "type": "SampleMetrics[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json", "id": "gem_well_alignment_metrics", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/barcode_counts.bcc.bincode", "id": "make_shard_bc_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "id": "barcode_counts", "type": "tbcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": false, "id": "no_star_alignments", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [], "id": "per_read_gap_align", "type": "parquet[]", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ALIGN_AND_COUNT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian align_and_count", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 6, "__vmem_gb": 9 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/feature_counts.fbc.bincode", "id": "feature_counts", "type": "fbc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_exons", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": false, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligner", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 30, "id": "transcriptome_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_polya_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_tso_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeted_umi_min_read_count", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "id": "total_barcode_counts", "type": "tbcc.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcode_subset", "type": "blf.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chevron_correction_factor", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chevron_affected_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "id": "counts_bc_order", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "probe_barcode_counts", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "id": "bc_umi_info", "type": "bui[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "id": "pos_sorted", "type": "asf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "id": "bam_header", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "id": "barcode_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "annotation_files", "type": "AnnotationFiles", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [], "id": "per_read_gap_align", "type": "parquet[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": false, "id": "no_star_alignments", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 11, "__threads": 4, "__vmem_gb": 14, "range": { "end": { "content": { "Sequence": "CCTACGTCTCTACCAC" }, "gem_group": 1, "valid": false }, "start": null }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 }, { "chunkDef": { "__mem_gb": 11, "__threads": 4, "__vmem_gb": 14, "range": { "end": { "content": { "Sequence": "GGGTGATTAGATAACA" }, "gem_group": 1, "valid": false }, "start": { "content": { "Sequence": "CCTACGTCTCTACCAC" }, "gem_group": 1, "valid": false } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 1 }, { "chunkDef": { "__mem_gb": 11, "__threads": 4, "__vmem_gb": 14, "range": { "end": { "content": { "Sequence": "TGTCGACCAATTGGTA" }, "gem_group": 1, "valid": false }, "start": { "content": { "Sequence": "GGGTGATTAGATAACA" }, "gem_group": 1, "valid": false } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 2 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "AATGACCGTGGTCAAG" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "TGTCGACCAATTGGTA" }, "gem_group": 1, "valid": false } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 3 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "ACTATTCCAAACTCGT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "AATGACCGTGGTCAAG" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 4 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "AGGAATAAGATGGTAT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "ACTATTCCAAACTCGT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 5 }, { "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": { "content": { "Sequence": "AGTGATCTCACTGGTA" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "AGGAATAAGATGGTAT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 6 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "ATGAAAGAGACCTCCG" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "AGTGATCTCACTGGTA" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 7 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "CAAGACTTCACAACCA" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "ATGAAAGAGACCTCCG" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 8 }, { "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": { "content": { "Sequence": "CAGCACGTCCATGCAA" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CAAGACTTCACAACCA" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 9 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "CATTCCGAGGGAGAAT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CAGCACGTCCATGCAA" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 10 }, { "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": { "content": { "Sequence": "CCGGACATCTGATGGT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CATTCCGAGGGAGAAT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 11 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "CGAGTGCTCTGACCCT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CCGGACATCTGATGGT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 12 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "CTAACTTGTGCCTTCT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CGAGTGCTCTGACCCT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 13 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "CTCCTTTGTTTCCATT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CTAACTTGTGCCTTCT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 14 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "CTTCTAACATAGGAGC" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CTCCTTTGTTTCCATT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 15 }, { "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": { "content": { "Sequence": "GACTATGTCATGGTAC" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "CTTCTAACATAGGAGC" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 16 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "GATGACTCAAAGAACT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "GACTATGTCATGGTAC" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 17 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "GCCCGAAGTGGTCTAT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "GATGACTCAAAGAACT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 18 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "GGCACGTGTCACAGTT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "GCCCGAAGTGGTCTAT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 19 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "GGTAGAGTCGAGGCAA" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "GGCACGTGTCACAGTT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 20 }, { "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": { "content": { "Sequence": "GTCACTCTCATGCCAA" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "GGTAGAGTCGAGGCAA" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 21 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "GTGGTTAGTGGAGAAA" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "GTCACTCTCATGCCAA" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 22 }, { "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": { "content": { "Sequence": "TAAGCCATCGTGTCAA" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "GTGGTTAGTGGAGAAA" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 23 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "TAGGTTGAGCCTTCTC" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "TAAGCCATCGTGTCAA" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 24 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "TCAGGGCCATGAAAGT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "TAGGTTGAGCCTTCTC" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 25 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "TCCTCTTGTCGTTGCG" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "TCAGGGCCATGAAAGT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 26 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "TGACAGTTCTAGTCAG" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "TCCTCTTGTCGTTGCG" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 27 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "TGGAACTTCTAGTGTG" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "TGACAGTTCTAGTCAG" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 28 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": { "content": { "Sequence": "TTAGGCATCATTTCGT" }, "gem_group": 1, "valid": true }, "start": { "content": { "Sequence": "TGGAACTTCTAGTGTG" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 29 }, { "chunkDef": { "__mem_gb": 13, "__threads": 4, "__vmem_gb": 16, "range": { "end": null, "start": { "content": { "Sequence": "TTAGGCATCATTTCGT" }, "gem_group": 1, "valid": true } }, "read_ann_subsample_rate": 0.10739576816558838 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 30 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BARCODE_CORRECTION", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian barcode_correction", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 6, "__vmem_gb": 9 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/barcode_counts.bcc.bincode", "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/barcode_segment_counts.bsc.bincode", "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/invalid.shard" ], "id": "invalid_uncorrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/bc_correct_summary.bcm.bincode", "id": "valid_read_metrics", "type": "bcm.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1000, "id": "min_reads_to_report_bc", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_CORRECTION_MAP", "matchedFork": null, "value": null, "id": "correction_map", "type": "cmf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_under_tissue", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "id": "valid_corrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/correct_barcode_counts.bcc.bincode", "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "id": "total_barcode_counts", "type": "tbcc.bincode", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 0 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 1 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 1 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 2 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 2 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 3 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 3 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 4 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 5 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 5 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 6 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 6 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 7 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 7 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 8 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 8 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 9 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 9 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 10 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 10 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 11 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 11 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 12 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 12 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 13 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 13 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 14 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 14 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 15 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 15 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 16 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 16 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 17 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 17 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 18 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 18 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 19 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 19 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 20 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 20 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 21 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 21 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 22 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 22 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 23 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 23 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 24 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 24 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 25 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 25 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 26 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 26 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 27 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 27 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 28 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 28 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 29 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 29 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 30 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 30 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 31 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 31 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 32 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 32 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 33 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 33 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 34 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 34 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 35 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 35 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 36 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 36 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 37 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 37 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 38 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 38 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 39 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 39 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 40 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 40 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 41 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 41 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 42 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 42 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 43 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 43 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 44 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 44 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 45 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 45 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 46 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 46 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 47 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 47 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 48 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 48 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 49 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 49 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 50 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 50 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 51 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 51 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 52 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 52 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 53 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 53 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 54 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 54 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 55 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 55 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 56 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 56 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 57 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 57 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 58 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 58 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 59 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 59 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 60 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 60 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 61 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 61 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 62 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 62 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 63 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 63 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 64 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 64 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 65 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 65 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 66 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 66 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 67 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 67 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 68 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 68 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 69 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 69 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 70 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 70 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 71 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 71 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 72 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 72 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 73 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 73 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 74 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 74 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 75 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 75 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 76 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 76 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 77 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 77 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 78 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 78 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 79 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 79 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 80 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 80 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 81 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 81 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 82 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 82 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 83 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 83 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 84 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 84 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 85 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 85 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 86 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 86 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 87 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 87 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 88 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 88 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 89 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 89 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 90 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 90 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 91 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 91 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 92 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 92 }, { "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "count": 501408, "index": 93 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 93 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_CORRECTION_MAP", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "COLLATE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian collate_metrics", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "id": "per_barcode_metrics", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": null, "id": "multi_metrics", "type": "SampleMetrics[]", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "sample": "non_multiplexed" }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "COMPUTE_CORRECTION_FACTOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COMPUTE_CORRECTION_FACTOR", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COMPUTE_CORRECTION_FACTOR", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/spatial/compute_correction_factor", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COMPUTE_CORRECTION_FACTOR/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COMPUTE_CORRECTION_FACTOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COMPUTE_CORRECTION_FACTOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "v1_pattern_fix", "type": "V1PatternFixArgs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_under_tissue", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "correction_factor", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "affected_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_downsampling", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.DISABLE_CORRECTION_FACTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COMPUTE_CORRECTION_FACTOR" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "DISABLE_CORRECTION_FACTOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.DISABLE_CORRECTION_FACTOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/DISABLE_CORRECTION_FACTOR", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/DISABLE_CORRECTION_FACTOR", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/spatial/disable_correction_factor", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/DISABLE_CORRECTION_FACTOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/DISABLE_CORRECTION_FACTOR/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/DISABLE_CORRECTION_FACTOR/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "v1_pattern_fix", "type": "V1PatternFixArgs", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.DISABLE_CORRECTION_FACTOR", "matchedFork": null, "value": true, "id": "disable_correction_factor", "type": "bool", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/DISABLE_CORRECTION_FACTOR/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [], "stagecodeLang": "Python", "type": "stage" }, { "name": "MAKE_CORRECTION_MAP", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_CORRECTION_MAP", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_CORRECTION_MAP", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_CORRECTION_MAP", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian make_correction_map", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_CORRECTION_MAP/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_CORRECTION_MAP/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_CORRECTION_MAP/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/barcode_segment_counts.bsc.bincode", "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_CORRECTION_MAP", "matchedFork": null, "value": null, "id": "correction_map", "type": "cmf.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_CORRECTION_MAP" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_CORRECTION_MAP" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_READ_SHARDS_STRUCT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ], "id": "valid_reads", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "id": "corrected_reads", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "id": "invalid_reads", "type": "shard[]", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "id": "read_shards", "type": "ReadShards", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "MAKE_SHARD", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian make_shard", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 9, "__vmem_gb": 12 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_read_pairs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_features", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference_path", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ], "id": "valid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/invalid.shard" ], "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/barcode_counts.bcc.bincode", "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/barcode_segment_counts.bsc.bincode", "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/feature_counts.fbc.bincode", "id": "feature_counts", "type": "fbc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/summary.json", "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": 465567671, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/bc_correct_summary.bcm.bincode", "id": "bc_correct_summary", "type": "bcm.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "id": "sequencing_metrics", "type": "smf.json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "chunk_id": 0, "feature_reference": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode" }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/summary.json", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/summary.json", null, "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/summary.json", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json" ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3049cf9433/files/summary.json", "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.COLLATE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_BARCODE_INDEX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_barcode_index", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/correct_barcode_counts.bcc.bincode", "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_under_tissue", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/summary.json", "id": "barcode_correction_summary", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_BARCODE_SUMMARY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_barcode_summary", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/summary.json", "id": "barcode_correction_summary", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary", "type": "h5", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_H5_MATRIX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_h5_matrix", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "id": "counts", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/summary.json", "id": "barcode_correction_summary", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "id": "matrix", "type": "h5", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_H5_MATRIX" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_MATRIX_MARKET", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_matrix_market", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "id": "counts", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "id": "barcode_index", "type": "bi.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/summary.json", "id": "barcode_correction_summary", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "id": "feature_bc_matrix", "type": "path", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_MATRIX_MARKET" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "_SLFE_PARTIAL_FIRST_PASS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/feature_counts.fbc.bincode", "id": "feature_counts", "type": "fbc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligner", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_polya_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_tso_min_score", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "id": "total_barcode_counts", "type": "tbcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/correct_barcode_counts.bcc.bincode", "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umi_read_count_threshold", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umi_filtering_summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SET_TARGETED_UMI_FILTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "INITIAL_ALIGN_AND_COUNT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/INITIAL_ALIGN_AND_COUNT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/INITIAL_ALIGN_AND_COUNT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian align_and_count", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/INITIAL_ALIGN_AND_COUNT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/INITIAL_ALIGN_AND_COUNT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/INITIAL_ALIGN_AND_COUNT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/feature_counts.fbc.bincode", "id": "feature_counts", "type": "fbc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_exons", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "no_bam", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aligner", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 30, "id": "transcriptome_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_polya_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 20, "id": "trim_tso_min_score", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeted_umi_min_read_count", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "id": "total_barcode_counts", "type": "tbcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SUBSAMPLE_BARCODES", "matchedFork": null, "value": null, "id": "barcode_subset", "type": "blf.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chevron_correction_factor", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chevron_affected_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "counts_bc_order", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "probe_barcode_counts", "type": "csf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "bc_umi_info", "type": "bui[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "pos_sorted", "type": "asf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "bam_header", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "barcode_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "annotation_files", "type": "AnnotationFiles", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "per_read_gap_align", "type": "parquet[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "per_barcode_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "no_star_alignments", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SUBSAMPLE_BARCODES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SET_TARGETED_UMI_FILTER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SET_TARGETED_UMI_FILTER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SET_TARGETED_UMI_FILTER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SET_TARGETED_UMI_FILTER", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian set_targeted_umi_filter", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SET_TARGETED_UMI_FILTER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SET_TARGETED_UMI_FILTER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SET_TARGETED_UMI_FILTER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "matchedFork": null, "value": null, "id": "bc_umi_info", "type": "bui[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "id": "feature_reference", "type": "frf.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SET_TARGETED_UMI_FILTER", "matchedFork": null, "value": null, "id": "umi_read_count_threshold", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SET_TARGETED_UMI_FILTER", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SET_TARGETED_UMI_FILTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.INITIAL_ALIGN_AND_COUNT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SET_TARGETED_UMI_FILTER" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSAMPLE_BARCODES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SUBSAMPLE_BARCODES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SUBSAMPLE_BARCODES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SUBSAMPLE_BARCODES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian subsample_barcodes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SUBSAMPLE_BARCODES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SUBSAMPLE_BARCODES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/SUBSAMPLE_BARCODES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/correct_barcode_counts.bcc.bincode", "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SUBSAMPLE_BARCODES", "matchedFork": null, "value": null, "id": "barcode_subset", "type": "blf.json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS.SUBSAMPLE_BARCODES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_VDJ_FILTER_SWITCH", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/MAKE_VDJ_FILTER_SWITCH", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/MAKE_VDJ_FILTER_SWITCH", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian make_filter_switch", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/MAKE_VDJ_FILTER_SWITCH/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/MAKE_VDJ_FILTER_SWITCH/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/MAKE_VDJ_FILTER_SWITCH/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_count", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multiplet_filter", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "shared_contig_filter", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "umi_baseline_filter", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/MAKE_VDJ_FILTER_SWITCH/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VDJ_B_GEM_WELL_PROCESSOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inputs", "type": "VdjAssemblerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "matchedFork": null, "value": true, "id": "has_no_vdj_ref", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gex_cells_per_tag", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "setup_chunks_outs", "type": "MULTI_SETUP_CHUNKS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "assembler_outs", "type": "SC_VDJ_CONTIG_ASSEMBLER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "lib_level", "type": "VDJ_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_sample", "type": "map\u003cVDJ_ANALYZER\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_ws_contents", "type": "map\u003cvwc.json\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian build_per_sample_vdj_ws_contents", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "lib_level_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "physical_library_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "lib_level_vdj_ws_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_vdj_ws_json", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "filter_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_cells_per_tag_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_ws_contents", "type": "map\u003cvwc.json\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "LIB_VDJ_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": false, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "asm_contig_annotations": null, "assemblable_reads_per_bc": null, "barcode_brief": null, "barcode_full": null, "barcode_support": null, "corrected_barcode_counts": null, "n50_n50_rpu": null, "summary": null, "summary_tsv": null, "total_read_pairs": null, "umi_summary_tsv": null }, "id": "assembler_outs", "type": "VdjAssemblerAnalyzerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "airr_rearrangement": null, "all_contig_annotations_csv": null, "all_contig_annotations_json": null, "clonotypes_csv": null, "concat_ref_bam": null, "concat_ref_bam_bai": null, "concat_ref_fasta": null, "concat_ref_fasta_fai": null, "consensus_annotations_csv": null, "consensus_bam": null, "consensus_bam_bai": null, "consensus_fasta": null, "consensus_fasta_fai": null, "donor_ref_fa": null, "enclone_output": null, "filtered_contig_annotations_csv": null }, "id": "clonotype", "type": "VdjAnalyzerClonotypeOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "beam_analyzer", "type": "BeamAnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "all_contig_barcodes": null, "annotations_bed": null, "barcode_brief": null, "cdr3_barcodes": null, "cell_barcodes": null, "contig_fasta": null, "contig_fasta_fai": null, "contig_fastq": null, "filter_metrics": null, "filter_summary": null, "filtered_contig_fasta": null, "filtered_contig_fastq": null, "metrics_summary_csv": null, "metrics_summary_json": null, "per_bc_filters": null, "productive_barcodes": null, "productive_cell_barcodes": null, "report": null, "umi_summary": null, "vdj_contig_info": null, "vloupe": null, "web_summary": null, "web_summary_data": null }, "id": "report", "type": "VdjReport", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "report", "type": "txt", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BEAM_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "outputs", "type": "BeamAnalyzerOutputs", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALCULATE_ANTIGEN_SPECIFICITY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/antigen_specificity", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_assignment", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "clonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "exact_subclonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COMPUTE_ANTIGEN_VDJ_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian compute_antigen_vdj_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_bin", "type": "ag.vdj.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CREATE_BARCODE_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian create_barcode_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "gex_filtered_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "vdj_filtered_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "matchedFork": null, "value": null, "id": "per_barcode_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CLONOTYPE_ASSIGNER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "airr_rearrangement", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CREATE_AIRR_TSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian airr_filter", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "matchedFork": null, "value": null, "id": "airr_annotations", "type": "tsv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILL_CLONOTYPE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian fill_clonotype_info", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_ENCLONE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assigner", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CLONOTYPE_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_clonotype_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONCAT_REF_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_concat_ref_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_bam", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_TXT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_txt", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILTER_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian filter_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_NO_CLONOTYPING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_no_clonotyping", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "merged_liblevel": null, "post_cell_filtering": null, "post_clonotyping": null }, "id": "contigs", "type": "ContigAnnotationSource", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "final_contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian make_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "REPORT_CONTIGS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/report_contigs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contigs", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "", "id": "prefix", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SETUP_VDJ_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": false, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "lib_level_gex", "type": "GexMatrices", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_cell_calling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_beam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_asm_metrics", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSET_ASSEMBLY_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian subset_assembly_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "per_sample", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_FILTERS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian summarize_vdj_filters", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_description", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "html", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_bc_filters", "type": "parquet", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/summarize_reports", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotype_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary_data", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "VDJ_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_call_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_GEX_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_gex_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VLOUPE_PREPROCESS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vloupe/vloupe_preprocess", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "SC_VDJ_ASSEMBLER_CS", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "feature_barcode_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_controls", "type": "map\u003cstring\u003e", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "matchedFork": null, "value": null, "id": "output_for_vloupe", "type": "vloupe", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_ANN_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_ann_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "all_contig_annotations_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_contig_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "annotations_bed", "type": "bed", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "all_contig_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_PROTO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_aggr martian write_contig_proto", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_wells", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_contig_info", "type": "pb", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MERGE_PER_SAMPLE_ANNOTATIONS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian merge_per_sample_annotations", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_annotations", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gex_cells_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_cells_per_tag_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTI_SETUP_CHUNKS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian multi_setup_chunks", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "VDJ", "id": "default_library_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_def", "type": "map[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "barcode_whitelists", "type": "string[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "visium_hd_slide_name", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "PER_SAMPLE_VDJ_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": true, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "asm_contig_annotations": null, "assemblable_reads_per_bc": null, "barcode_brief": null, "barcode_full": null, "barcode_support": null, "corrected_barcode_counts": null, "n50_n50_rpu": null, "summary": null, "summary_tsv": null, "total_read_pairs": null, "umi_summary_tsv": null }, "id": "assembler_outs", "type": "VdjAssemblerAnalyzerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "airr_rearrangement": null, "all_contig_annotations_csv": null, "all_contig_annotations_json": null, "clonotypes_csv": null, "concat_ref_bam": null, "concat_ref_bam_bai": null, "concat_ref_fasta": null, "concat_ref_fasta_fai": null, "consensus_annotations_csv": null, "consensus_bam": null, "consensus_bam_bai": null, "consensus_fasta": null, "consensus_fasta_fai": null, "donor_ref_fa": null, "enclone_output": null, "filtered_contig_annotations_csv": null }, "id": "clonotype", "type": "VdjAnalyzerClonotypeOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "beam_analyzer", "type": "BeamAnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "all_contig_barcodes": null, "annotations_bed": null, "barcode_brief": null, "cdr3_barcodes": null, "cell_barcodes": null, "contig_fasta": null, "contig_fasta_fai": null, "contig_fastq": null, "filter_metrics": null, "filter_summary": null, "filtered_contig_fasta": null, "filtered_contig_fastq": null, "metrics_summary_csv": null, "metrics_summary_json": null, "per_bc_filters": null, "productive_barcodes": null, "productive_cell_barcodes": null, "report": null, "umi_summary": null, "vdj_contig_info": null, "vloupe": null, "web_summary": null, "web_summary_data": null }, "id": "report", "type": "VdjReport", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "report", "type": "txt", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BEAM_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "outputs", "type": "BeamAnalyzerOutputs", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALCULATE_ANTIGEN_SPECIFICITY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/antigen_specificity", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_assignment", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "clonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "exact_subclonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COMPUTE_ANTIGEN_VDJ_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian compute_antigen_vdj_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_bin", "type": "ag.vdj.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CREATE_BARCODE_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian create_barcode_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "gex_filtered_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "vdj_filtered_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "matchedFork": null, "value": null, "id": "per_barcode_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CLONOTYPE_ASSIGNER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "airr_rearrangement", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CREATE_AIRR_TSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian airr_filter", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "matchedFork": null, "value": null, "id": "airr_annotations", "type": "tsv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILL_CLONOTYPE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian fill_clonotype_info", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_ENCLONE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assigner", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CLONOTYPE_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_clonotype_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONCAT_REF_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_concat_ref_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_bam", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_TXT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_txt", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILTER_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian filter_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_NO_CLONOTYPING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_no_clonotyping", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "merged_liblevel": null, "post_cell_filtering": null, "post_clonotyping": null }, "id": "contigs", "type": "ContigAnnotationSource", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "final_contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian make_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "REPORT_CONTIGS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/report_contigs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contigs", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "", "id": "prefix", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SETUP_VDJ_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": true, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "lib_level_gex", "type": "GexMatrices", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_cell_calling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_beam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_asm_metrics", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSET_ASSEMBLY_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian subset_assembly_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "per_sample", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_FILTERS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian summarize_vdj_filters", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_description", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "html", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_bc_filters", "type": "parquet", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/summarize_reports", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotype_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary_data", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "VDJ_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_call_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_GEX_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_gex_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VLOUPE_PREPROCESS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vloupe/vloupe_preprocess", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "SC_VDJ_ASSEMBLER_CS", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "feature_barcode_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_controls", "type": "map\u003cstring\u003e", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "matchedFork": null, "value": null, "id": "output_for_vloupe", "type": "vloupe", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_ANN_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_ann_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "all_contig_annotations_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_contig_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "annotations_bed", "type": "bed", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "all_contig_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_PROTO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_aggr martian write_contig_proto", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_wells", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_contig_info", "type": "pb", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SC_VDJ_CONTIG_ASSEMBLER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_folder", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_contig_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_reads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": null, "invalid_reads": null, "valid_reads": null }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "raw_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "processed_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcodes_in_chunks", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "unmapped_sample_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASSEMBLE_VDJ", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assembly", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "bc_sorted_rna_reads", "type": "bincode.lz4[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "npairs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_contig_length", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcodes_in_chunks", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "align_info", "type": "txt", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "unmapped_sample_fastq", "type": "fastq", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BARCODE_CORRECTION", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian barcode_correction", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "invalid_uncorrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid_read_metrics", "type": "bcm.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1000, "id": "min_reads_to_report_bc", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "correction_map", "type": "cmf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_under_tissue", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "valid_corrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "total_barcode_counts", "type": "tbcc.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_SHARD", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian make_shard", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_read_pairs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_features", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference_path", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "feature_counts", "type": "fbc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "bc_correct_summary", "type": "bcm.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUST_BRIDGE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian rust_bridge", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid_uncorrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "valid_corrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "raw_barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "bc_sorted_rna_reads", "type": "bincode.lz4[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "barcodes", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "raw_barcode_counts_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "processed_read_pairs", "type": "int", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SETUP_VDJ_DEMUX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_demux", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_B_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "is_not_multi", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "has_antigen", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "per_sample_info", "type": "map\u003cVdjDemuxSampleInfo\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VDJ_T_GD_GEM_WELL_PROCESSOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inputs", "type": "VdjAssemblerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "matchedFork": null, "value": true, "id": "has_no_vdj_ref", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gex_cells_per_tag", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "setup_chunks_outs", "type": "MULTI_SETUP_CHUNKS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "assembler_outs", "type": "SC_VDJ_CONTIG_ASSEMBLER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "lib_level", "type": "VDJ_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_sample", "type": "map\u003cVDJ_ANALYZER\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_ws_contents", "type": "map\u003cvwc.json\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian build_per_sample_vdj_ws_contents", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "lib_level_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "physical_library_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "lib_level_vdj_ws_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_vdj_ws_json", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "filter_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_cells_per_tag_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_ws_contents", "type": "map\u003cvwc.json\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "LIB_VDJ_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": false, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "asm_contig_annotations": null, "assemblable_reads_per_bc": null, "barcode_brief": null, "barcode_full": null, "barcode_support": null, "corrected_barcode_counts": null, "n50_n50_rpu": null, "summary": null, "summary_tsv": null, "total_read_pairs": null, "umi_summary_tsv": null }, "id": "assembler_outs", "type": "VdjAssemblerAnalyzerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "airr_rearrangement": null, "all_contig_annotations_csv": null, "all_contig_annotations_json": null, "clonotypes_csv": null, "concat_ref_bam": null, "concat_ref_bam_bai": null, "concat_ref_fasta": null, "concat_ref_fasta_fai": null, "consensus_annotations_csv": null, "consensus_bam": null, "consensus_bam_bai": null, "consensus_fasta": null, "consensus_fasta_fai": null, "donor_ref_fa": null, "enclone_output": null, "filtered_contig_annotations_csv": null }, "id": "clonotype", "type": "VdjAnalyzerClonotypeOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "beam_analyzer", "type": "BeamAnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "all_contig_barcodes": null, "annotations_bed": null, "barcode_brief": null, "cdr3_barcodes": null, "cell_barcodes": null, "contig_fasta": null, "contig_fasta_fai": null, "contig_fastq": null, "filter_metrics": null, "filter_summary": null, "filtered_contig_fasta": null, "filtered_contig_fastq": null, "metrics_summary_csv": null, "metrics_summary_json": null, "per_bc_filters": null, "productive_barcodes": null, "productive_cell_barcodes": null, "report": null, "umi_summary": null, "vdj_contig_info": null, "vloupe": null, "web_summary": null, "web_summary_data": null }, "id": "report", "type": "VdjReport", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "report", "type": "txt", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BEAM_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "outputs", "type": "BeamAnalyzerOutputs", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALCULATE_ANTIGEN_SPECIFICITY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/antigen_specificity", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_assignment", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "clonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "exact_subclonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COMPUTE_ANTIGEN_VDJ_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian compute_antigen_vdj_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_bin", "type": "ag.vdj.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CREATE_BARCODE_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian create_barcode_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "gex_filtered_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "vdj_filtered_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "matchedFork": null, "value": null, "id": "per_barcode_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CLONOTYPE_ASSIGNER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "airr_rearrangement", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CREATE_AIRR_TSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian airr_filter", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "matchedFork": null, "value": null, "id": "airr_annotations", "type": "tsv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILL_CLONOTYPE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian fill_clonotype_info", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_ENCLONE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assigner", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CLONOTYPE_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_clonotype_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONCAT_REF_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_concat_ref_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_bam", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_TXT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_txt", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILTER_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian filter_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_NO_CLONOTYPING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_no_clonotyping", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "merged_liblevel": null, "post_cell_filtering": null, "post_clonotyping": null }, "id": "contigs", "type": "ContigAnnotationSource", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "final_contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian make_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "REPORT_CONTIGS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/report_contigs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contigs", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "", "id": "prefix", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SETUP_VDJ_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": false, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "lib_level_gex", "type": "GexMatrices", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_cell_calling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_beam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_asm_metrics", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSET_ASSEMBLY_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian subset_assembly_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "per_sample", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_FILTERS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian summarize_vdj_filters", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_description", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "html", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_bc_filters", "type": "parquet", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/summarize_reports", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotype_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary_data", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "VDJ_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_call_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_GEX_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_gex_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VLOUPE_PREPROCESS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vloupe/vloupe_preprocess", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "SC_VDJ_ASSEMBLER_CS", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "feature_barcode_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_controls", "type": "map\u003cstring\u003e", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "matchedFork": null, "value": null, "id": "output_for_vloupe", "type": "vloupe", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_ANN_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_ann_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "all_contig_annotations_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_contig_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "annotations_bed", "type": "bed", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "all_contig_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_PROTO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_aggr martian write_contig_proto", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_wells", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_contig_info", "type": "pb", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MERGE_PER_SAMPLE_ANNOTATIONS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian merge_per_sample_annotations", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_annotations", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gex_cells_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_cells_per_tag_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTI_SETUP_CHUNKS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian multi_setup_chunks", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "VDJ", "id": "default_library_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_def", "type": "map[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "barcode_whitelists", "type": "string[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "visium_hd_slide_name", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "PER_SAMPLE_VDJ_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": true, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "asm_contig_annotations": null, "assemblable_reads_per_bc": null, "barcode_brief": null, "barcode_full": null, "barcode_support": null, "corrected_barcode_counts": null, "n50_n50_rpu": null, "summary": null, "summary_tsv": null, "total_read_pairs": null, "umi_summary_tsv": null }, "id": "assembler_outs", "type": "VdjAssemblerAnalyzerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "airr_rearrangement": null, "all_contig_annotations_csv": null, "all_contig_annotations_json": null, "clonotypes_csv": null, "concat_ref_bam": null, "concat_ref_bam_bai": null, "concat_ref_fasta": null, "concat_ref_fasta_fai": null, "consensus_annotations_csv": null, "consensus_bam": null, "consensus_bam_bai": null, "consensus_fasta": null, "consensus_fasta_fai": null, "donor_ref_fa": null, "enclone_output": null, "filtered_contig_annotations_csv": null }, "id": "clonotype", "type": "VdjAnalyzerClonotypeOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "beam_analyzer", "type": "BeamAnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "all_contig_barcodes": null, "annotations_bed": null, "barcode_brief": null, "cdr3_barcodes": null, "cell_barcodes": null, "contig_fasta": null, "contig_fasta_fai": null, "contig_fastq": null, "filter_metrics": null, "filter_summary": null, "filtered_contig_fasta": null, "filtered_contig_fastq": null, "metrics_summary_csv": null, "metrics_summary_json": null, "per_bc_filters": null, "productive_barcodes": null, "productive_cell_barcodes": null, "report": null, "umi_summary": null, "vdj_contig_info": null, "vloupe": null, "web_summary": null, "web_summary_data": null }, "id": "report", "type": "VdjReport", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "report", "type": "txt", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BEAM_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "outputs", "type": "BeamAnalyzerOutputs", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALCULATE_ANTIGEN_SPECIFICITY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/antigen_specificity", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_assignment", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "clonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "exact_subclonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COMPUTE_ANTIGEN_VDJ_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian compute_antigen_vdj_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_bin", "type": "ag.vdj.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CREATE_BARCODE_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian create_barcode_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "gex_filtered_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "vdj_filtered_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "matchedFork": null, "value": null, "id": "per_barcode_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CLONOTYPE_ASSIGNER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "airr_rearrangement", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CREATE_AIRR_TSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian airr_filter", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "matchedFork": null, "value": null, "id": "airr_annotations", "type": "tsv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILL_CLONOTYPE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian fill_clonotype_info", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_ENCLONE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assigner", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CLONOTYPE_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_clonotype_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONCAT_REF_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_concat_ref_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_bam", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_TXT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_txt", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILTER_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian filter_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_NO_CLONOTYPING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_no_clonotyping", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "merged_liblevel": null, "post_cell_filtering": null, "post_clonotyping": null }, "id": "contigs", "type": "ContigAnnotationSource", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "final_contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian make_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "REPORT_CONTIGS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/report_contigs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contigs", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "", "id": "prefix", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SETUP_VDJ_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": true, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "lib_level_gex", "type": "GexMatrices", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_cell_calling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_beam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_asm_metrics", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSET_ASSEMBLY_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian subset_assembly_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "per_sample", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_FILTERS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian summarize_vdj_filters", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_description", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "html", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_bc_filters", "type": "parquet", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/summarize_reports", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotype_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary_data", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "VDJ_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_call_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_GEX_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_gex_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VLOUPE_PREPROCESS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vloupe/vloupe_preprocess", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "SC_VDJ_ASSEMBLER_CS", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "feature_barcode_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_controls", "type": "map\u003cstring\u003e", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "matchedFork": null, "value": null, "id": "output_for_vloupe", "type": "vloupe", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_ANN_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_ann_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "all_contig_annotations_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_contig_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "annotations_bed", "type": "bed", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "all_contig_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_PROTO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_aggr martian write_contig_proto", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_wells", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_contig_info", "type": "pb", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SC_VDJ_CONTIG_ASSEMBLER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_folder", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_contig_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_reads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": null, "invalid_reads": null, "valid_reads": null }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "raw_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "processed_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcodes_in_chunks", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "unmapped_sample_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASSEMBLE_VDJ", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assembly", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "bc_sorted_rna_reads", "type": "bincode.lz4[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "npairs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_contig_length", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcodes_in_chunks", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "align_info", "type": "txt", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "unmapped_sample_fastq", "type": "fastq", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BARCODE_CORRECTION", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian barcode_correction", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "invalid_uncorrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid_read_metrics", "type": "bcm.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1000, "id": "min_reads_to_report_bc", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "correction_map", "type": "cmf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_under_tissue", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "valid_corrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "total_barcode_counts", "type": "tbcc.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_SHARD", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian make_shard", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_read_pairs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_features", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference_path", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "feature_counts", "type": "fbc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "bc_correct_summary", "type": "bcm.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUST_BRIDGE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian rust_bridge", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid_uncorrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "valid_corrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "raw_barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "bc_sorted_rna_reads", "type": "bincode.lz4[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "barcodes", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "raw_barcode_counts_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "processed_read_pairs", "type": "int", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SETUP_VDJ_DEMUX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_demux", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GD_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "is_not_multi", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "has_antigen", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "per_sample_info", "type": "map\u003cVdjDemuxSampleInfo\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VDJ_T_GEM_WELL_PROCESSOR", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inputs", "type": "VdjAssemblerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG", "matchedFork": null, "value": true, "id": "has_no_vdj_ref", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gex_cells_per_tag", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "setup_chunks_outs", "type": "MULTI_SETUP_CHUNKS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "assembler_outs", "type": "SC_VDJ_CONTIG_ASSEMBLER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "lib_level", "type": "VDJ_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_sample", "type": "map\u003cVDJ_ANALYZER\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_ws_contents", "type": "map\u003cvwc.json\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian build_per_sample_vdj_ws_contents", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/BUILD_PER_SAMPLE_VDJ_WS_CONTENTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "lib_level_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "physical_library_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "lib_level_vdj_ws_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_vdj_ws_json", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "filter_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_cells_per_tag_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_ws_contents", "type": "map\u003cvwc.json\u003e", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.BUILD_PER_SAMPLE_VDJ_WS_CONTENTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "LIB_VDJ_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": false, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "asm_contig_annotations": null, "assemblable_reads_per_bc": null, "barcode_brief": null, "barcode_full": null, "barcode_support": null, "corrected_barcode_counts": null, "n50_n50_rpu": null, "summary": null, "summary_tsv": null, "total_read_pairs": null, "umi_summary_tsv": null }, "id": "assembler_outs", "type": "VdjAssemblerAnalyzerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "airr_rearrangement": null, "all_contig_annotations_csv": null, "all_contig_annotations_json": null, "clonotypes_csv": null, "concat_ref_bam": null, "concat_ref_bam_bai": null, "concat_ref_fasta": null, "concat_ref_fasta_fai": null, "consensus_annotations_csv": null, "consensus_bam": null, "consensus_bam_bai": null, "consensus_fasta": null, "consensus_fasta_fai": null, "donor_ref_fa": null, "enclone_output": null, "filtered_contig_annotations_csv": null }, "id": "clonotype", "type": "VdjAnalyzerClonotypeOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "beam_analyzer", "type": "BeamAnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "all_contig_barcodes": null, "annotations_bed": null, "barcode_brief": null, "cdr3_barcodes": null, "cell_barcodes": null, "contig_fasta": null, "contig_fasta_fai": null, "contig_fastq": null, "filter_metrics": null, "filter_summary": null, "filtered_contig_fasta": null, "filtered_contig_fastq": null, "metrics_summary_csv": null, "metrics_summary_json": null, "per_bc_filters": null, "productive_barcodes": null, "productive_cell_barcodes": null, "report": null, "umi_summary": null, "vdj_contig_info": null, "vloupe": null, "web_summary": null, "web_summary_data": null }, "id": "report", "type": "VdjReport", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/ASM_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "report", "type": "txt", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BEAM_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "outputs", "type": "BeamAnalyzerOutputs", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALCULATE_ANTIGEN_SPECIFICITY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/antigen_specificity", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_assignment", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "clonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "exact_subclonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COMPUTE_ANTIGEN_VDJ_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian compute_antigen_vdj_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_bin", "type": "ag.vdj.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CREATE_BARCODE_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian create_barcode_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "gex_filtered_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "vdj_filtered_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "matchedFork": null, "value": null, "id": "per_barcode_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CLONOTYPE_ASSIGNER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "airr_rearrangement", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CREATE_AIRR_TSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian airr_filter", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "matchedFork": null, "value": null, "id": "airr_annotations", "type": "tsv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILL_CLONOTYPE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian fill_clonotype_info", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_ENCLONE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assigner", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CLONOTYPE_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_clonotype_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONCAT_REF_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_concat_ref_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_bam", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_TXT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_txt", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILTER_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian filter_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_NO_CLONOTYPING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_no_clonotyping", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "merged_liblevel": null, "post_cell_filtering": null, "post_clonotyping": null }, "id": "contigs", "type": "ContigAnnotationSource", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "final_contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian make_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "REPORT_CONTIGS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/report_contigs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/REPORT_CONTIGS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contigs", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "", "id": "prefix", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SETUP_VDJ_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": false, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "lib_level_gex", "type": "GexMatrices", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_cell_calling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_beam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_asm_metrics", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSET_ASSEMBLY_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian subset_assembly_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "per_sample", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_FILTERS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian summarize_vdj_filters", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_description", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "html", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_bc_filters", "type": "parquet", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/summarize_reports", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotype_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary_data", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.REPORT_CONTIGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "VDJ_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_call_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_GEX_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_gex_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VLOUPE_PREPROCESS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vloupe/vloupe_preprocess", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "SC_VDJ_ASSEMBLER_CS", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "feature_barcode_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_controls", "type": "map\u003cstring\u003e", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS", "matchedFork": null, "value": null, "id": "output_for_vloupe", "type": "vloupe", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.VLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_ANN_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_ann_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "all_contig_annotations_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_ANN_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_contig_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "annotations_bed", "type": "bed", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "all_contig_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_PROTO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_aggr martian write_contig_proto", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/LIB_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_wells", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_contig_info", "type": "pb", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.LIB_VDJ_ANALYZER.WRITE_CONTIG_PROTO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MERGE_PER_SAMPLE_ANNOTATIONS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian merge_per_sample_annotations", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MERGE_PER_SAMPLE_ANNOTATIONS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": {}, "id": "per_sample_annotations", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gex_cells_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_cells_per_tag_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MERGE_PER_SAMPLE_ANNOTATIONS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTI_SETUP_CHUNKS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian multi_setup_chunks", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/MULTI_SETUP_CHUNKS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "VDJ", "id": "default_library_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_def", "type": "map[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "barcode_whitelists", "type": "string[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "visium_hd_slide_name", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "PER_SAMPLE_VDJ_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": true, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "asm_contig_annotations": null, "assemblable_reads_per_bc": null, "barcode_brief": null, "barcode_full": null, "barcode_support": null, "corrected_barcode_counts": null, "n50_n50_rpu": null, "summary": null, "summary_tsv": null, "total_read_pairs": null, "umi_summary_tsv": null }, "id": "assembler_outs", "type": "VdjAssemblerAnalyzerInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "library_level_gex", "type": "GexMatrices", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "airr_rearrangement": null, "all_contig_annotations_csv": null, "all_contig_annotations_json": null, "clonotypes_csv": null, "concat_ref_bam": null, "concat_ref_bam_bai": null, "concat_ref_fasta": null, "concat_ref_fasta_fai": null, "consensus_annotations_csv": null, "consensus_bam": null, "consensus_bam_bai": null, "consensus_fasta": null, "consensus_fasta_fai": null, "donor_ref_fa": null, "enclone_output": null, "filtered_contig_annotations_csv": null }, "id": "clonotype", "type": "VdjAnalyzerClonotypeOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "beam_analyzer", "type": "BeamAnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "all_contig_barcodes": null, "annotations_bed": null, "barcode_brief": null, "cdr3_barcodes": null, "cell_barcodes": null, "contig_fasta": null, "contig_fasta_fai": null, "contig_fastq": null, "filter_metrics": null, "filter_summary": null, "filtered_contig_fasta": null, "filtered_contig_fastq": null, "metrics_summary_csv": null, "metrics_summary_json": null, "per_bc_filters": null, "productive_barcodes": null, "productive_cell_barcodes": null, "report": null, "umi_summary": null, "vdj_contig_info": null, "vloupe": null, "web_summary": null, "web_summary_data": null }, "id": "report", "type": "VdjReport", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/ASM_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "report", "type": "txt", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BEAM_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "antigen_assignment": null, "antigen_specificity_scores": null, "antigen_vdj_metrics_bin": null, "antigen_vdj_metrics_json": null, "clonotype_concordance": null, "exact_subclonotype_concordance": null, "per_barcode": null, "specificity_summary": null }, "id": "outputs", "type": "BeamAnalyzerOutputs", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CALCULATE_ANTIGEN_SPECIFICITY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/feature/antigen_specificity", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CALCULATE_ANTIGEN_SPECIFICITY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_feature_counts_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "antigen_assignment", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "clonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "exact_subclonotype_concordance", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CALCULATE_ANTIGEN_SPECIFICITY" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "COMPUTE_ANTIGEN_VDJ_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian compute_antigen_vdj_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/COMPUTE_ANTIGEN_VDJ_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "vdj_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "id": "per_barcode_count_metrics", "type": "bmsf[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS", "matchedFork": null, "value": null, "id": "metrics_bin", "type": "ag.vdj.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.COMPUTE_ANTIGEN_VDJ_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CREATE_BARCODE_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian create_barcode_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/BEAM_ANALYZER/CREATE_BARCODE_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "gex_filtered_matrix", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "vdj_filtered_annotations", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "count_gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV", "matchedFork": null, "value": null, "id": "per_barcode_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER.CREATE_BARCODE_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "CLONOTYPE_ASSIGNER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "airr_rearrangement", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "CREATE_AIRR_TSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian airr_filter", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/CREATE_AIRR_TSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gem_well_map", "type": "map", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV", "matchedFork": null, "value": null, "id": "airr_annotations", "type": "tsv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.CREATE_AIRR_TSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILL_CLONOTYPE_INFO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian fill_clonotype_info", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/FILL_CLONOTYPE_INFO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUN_ENCLONE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assigner", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/RUN_ENCLONE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "donor_ref_fa", "type": "fa", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CLONOTYPE_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_clonotype_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CLONOTYPE_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS", "matchedFork": null, "value": null, "id": "clonotypes_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CLONOTYPE_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONCAT_REF_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_concat_ref_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONCAT_REF_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS", "matchedFork": null, "value": null, "id": "concat_ref_fasta_fai", "type": "fasta.fai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONCAT_REF_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_BAM", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_bam", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_BAM/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM", "matchedFork": null, "value": null, "id": "consensus_bam_bai", "type": "bam.bai", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.FILL_CLONOTYPE_INFO", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_BAM" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONSENSUS_TXT", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_consensus_txt", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/CLONOTYPE_ASSIGNER/WRITE_CONSENSUS_TXT/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT", "matchedFork": null, "value": null, "id": "consensus_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.RUN_ENCLONE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER.WRITE_CONSENSUS_TXT" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "FILTER_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian filter_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/FILTER_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_NO_CLONOTYPING", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_no_clonotyping", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/HANDLE_NO_CLONOTYPING/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "merged_liblevel": null, "post_cell_filtering": null, "post_clonotyping": null }, "id": "contigs", "type": "ContigAnnotationSource", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "final_contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_EXACT_CLONOTYPES", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian make_exact_clonotypes", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/MAKE_EXACT_CLONOTYPES/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "exact_clonotypes", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.MAKE_EXACT_CLONOTYPES" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "REPORT_CONTIGS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/report_contigs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/REPORT_CONTIGS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contigs", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "", "id": "prefix", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SETUP_VDJ_ANALYSIS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_analysis", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SETUP_VDJ_ANALYSIS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "denovo": null, "has_antigen": null, "has_no_vdj_ref": true, "is_multi": null, "per_sample": true, "skip_clonotyping": null }, "id": "vdj_config", "type": "VdjAnalysisConfig", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "demux_sample_info", "type": "VdjDemuxSampleInfo", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "raw_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5" }, "id": "lib_level_gex", "type": "GexMatrices", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_cell_calling", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_clonotyping", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_beam", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "disable_asm_metrics", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUBSET_ASSEMBLY_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian subset_assembly_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUBSET_ASSEMBLY_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "per_sample", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "merged_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "umi_summary", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_FILTERS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian summarize_vdj_filters", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_FILTERS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_description", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_barcode_fate", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "raw_matrix_h5", "type": "h5", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "filter_summary", "type": "html", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "metrics_summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_bc_filters", "type": "parquet", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.FILTER_EXACT_CLONOTYPES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SUMMARIZE_VDJ_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/summarize_reports", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/SUMMARIZE_VDJ_REPORTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null, null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "clonotype_summary", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "web_summary_data", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.ASM_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.REPORT_CONTIGS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_FILTERS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "VDJ_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_def", "type": "ChemistryDef", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "asm_filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASM_CALL_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian asm_call_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/ASM_CALL_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "vdj_chemistry_def", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "matchedFork": null, "value": { "asm_shared_contig": false, "enclone_cross": true, "enclone_multiplet": true, "enclone_shared_contig": false, "enclone_umi": false }, "id": "filter_switch", "type": "FilterSwitch", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "sample_fingerprint", "type": "fprint.json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "filter_diagnostics", "type": "json.lz4", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.MAKE_VDJ_FILTER_SWITCH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "HANDLE_GEX_CELLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian handle_gex_cells", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VDJ_CALL_CELLS/HANDLE_GEX_CELLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": false, "id": "is_antibody_only", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": true, "id": "is_non_targeted_gex", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.ASM_CALL_CELLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VDJ_CALL_CELLS.HANDLE_GEX_CELLS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "VLOUPE_PREPROCESS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vloupe/vloupe_preprocess", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/VLOUPE_PREPROCESS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "SC_VDJ_ASSEMBLER_CS", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "enclone_output", "type": "pb", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_vloupe", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "beam_mode", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "feature_barcode_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_scores", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity_controls", "type": "map\u003cstring\u003e", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS", "matchedFork": null, "value": null, "id": "output_for_vloupe", "type": "vloupe", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.CLONOTYPE_ASSIGNER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.VLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_ANN_CSV", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_ann_csv", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_ANN_CSV/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "all_contig_annotations_json", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "all_contig_annotations_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV", "matchedFork": null, "value": null, "id": "filtered_contig_annotations_csv", "type": "csv", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_ANN_CSV" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian write_contig_outs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_OUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "contig_fasta_fai", "type": "fasta.fai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "filtered_contig_fasta", "type": "fasta", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "annotations_bed", "type": "bed", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cell_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "paired_cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "prod_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cdr3_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "all_contig_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "WRITE_CONTIG_PROTO", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_aggr martian write_contig_proto", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/PER_SAMPLE_VDJ_ANALYZER/WRITE_CONTIG_PROTO/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "matchedFork": null, "value": null, "id": "contig_annotations_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "matchedFork": null, "value": null, "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "id": "gem_wells", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "matchedFork": null, "value": null, "id": "cell_barcodes", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config_sha", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_contig_info", "type": "pb", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.HANDLE_NO_CLONOTYPING", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SETUP_VDJ_ANALYSIS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUBSET_ASSEMBLY_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.SUMMARIZE_VDJ_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.PER_SAMPLE_VDJ_ANALYZER.WRITE_CONTIG_PROTO" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SC_VDJ_CONTIG_ASSEMBLER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_primers", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_folder", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_contig_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_reads", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": null, "invalid_reads": null, "valid_reads": null }, "id": "read_shards", "type": "ReadShards", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "raw_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "processed_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "asm_contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcodes_in_chunks", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "unmapped_sample_fastq", "type": "fastq", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "ASSEMBLE_VDJ", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_vdj martian assembly", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/ASSEMBLE_VDJ/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "bc_sorted_rna_reads", "type": "bincode.lz4[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "npairs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "receptor", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "denovo", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "inner_enrichment_primers", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_bc_counts", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "min_contig_length", "type": "int", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_bam_bai", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "umi_summary_tsv", "type": "tsv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "contig_annotations", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_brief", "type": "bdf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_full", "type": "bd.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcode_support", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "barcodes_in_chunks", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "assemblable_reads_per_bc", "type": "arp.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "align_info", "type": "txt", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ", "matchedFork": null, "value": null, "id": "unmapped_sample_fastq", "type": "fastq", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "BARCODE_CORRECTION", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian barcode_correction", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/BARCODE_CORRECTION/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "invalid_uncorrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid_read_metrics", "type": "bcm.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1000, "id": "min_reads_to_report_bc", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "correction_map", "type": "cmf.bincode", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcodes_under_tissue", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "valid_corrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "total_barcode_counts", "type": "tbcc.bincode", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MAKE_SHARD", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian make_shard", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "matchedFork": null, "value": null, "id": "read_chunks", "type": "map[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r1_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "r2_length", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "subsample_rate", "type": "float", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "initial_read_pairs", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_features", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference_path", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "invalid", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "barcode_segment_counts", "type": "bsc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "feature_counts", "type": "fbc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "total_read_pairs", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "feature_reference", "type": "frf.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "bc_correct_summary", "type": "bcm.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "sequencing_metrics", "type": "smf.json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MERGE_METRICS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian merge_metrics", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MERGE_METRICS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [ null, null, null ], "id": "summaries", "type": "json[]", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "RUST_BRIDGE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian rust_bridge", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/RUST_BRIDGE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "VDJ": null }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": 1, "id": "gem_well", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "valid_uncorrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "valid_corrected", "type": "shard[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "matchedFork": null, "value": null, "id": "raw_barcode_counts", "type": "bcc.bincode", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "matchedFork": null, "value": null, "id": "corrected_barcode_counts", "type": "bcc.bincode", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "bc_sorted_rna_reads", "type": "bincode.lz4[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "gem_groups", "type": "int[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "barcodes", "type": "json[]", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "raw_barcode_counts_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "corrected_barcode_counts_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "summary", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "n50_n50_rpu", "type": "int", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE", "matchedFork": null, "value": null, "id": "processed_read_pairs", "type": "int", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SETUP_VDJ_DEMUX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian setup_vdj_demux", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SETUP_VDJ_DEMUX/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "is_multi", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "is_not_multi", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "has_antigen", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "per_sample_info", "type": "map\u003cVdjDemuxSampleInfo\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX", "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "MULTI_REPORTER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_vdj_b": true, "disable_vdj_t": true, "disable_vdj_t_gd": true, "has_no_vdj_ref": true }, "id": "config", "type": "FullPipelineConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_RNA_COUNTER_CS", "id": "count_pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "basic_counter_outs": { "aggregate_barcodes": null, "alignments": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/pos_sorted.asf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/pos_sorted.asf" ], "annotation_files": null, "assign_tags": null, "bam_header": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/bam_header", "barcode_correction_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u3049cf66f7/files/barcode_summary.csv", "barcode_counts": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u3049cf66a9/files/total_barcode_counts.tbcc.bincode", "barcode_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u3049cf66f7/files/barcode_index.bi.bincode", "barcode_summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "bc_umi_info": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_umi_info.bui", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_umi_info.bui" ], "counts_bc_order": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/bc_sort.csf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/bc_sort.csf" ], "filtered_barcodes": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "filtered_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "filtered_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_mex", "gem_groups": [ 1 ], "gem_well_alignment_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/summary.json", "isotype_normalization_factors": null, "molecule_info": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u3049cfab39/files/molecule_info_non_multiplexed.h5", "multi_matrices": null, "multi_metrics": null, "multi_molecule_info": null, "multi_pos_sorted_bam": null, "no_star_alignments": false, "nonambient_cell_calls": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/nonambient_calls.csv", "per_barcode_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3049cf942a/files/per_barcode_metrics.csv", "per_barcode_metrics_shard": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3049cf66f8/files/metrics_shard.bmsf", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3049cf66f8/files/metrics_shard.bmsf" ], "per_probe_metrics": null, "per_read_gap_align": [], "possorted_genome_bai_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam.bai", "possorted_genome_bam": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/WRITE_POS_BAM/fork0/join-u3049cf9458/files/pos_sorted_non_multiplexed.bam", "possorted_genome_csi_index": null, "raw_gene_bc_matrices_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u3049cf942a/files/raw_feature_bc_matrix.h5", "raw_gene_bc_matrices_mex": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join-u3049cf942a/files/raw_feature_bc_matrix", "raw_probe_bc_matrix": null, "read_chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "read_shards": { "corrected_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/valid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/valid_shard.shard" ], "invalid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk29-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk30-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk31-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk32-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk33-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk34-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk35-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk36-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk37-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk38-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk39-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk40-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk41-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk42-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk43-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk44-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk45-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk46-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk47-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk48-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk49-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk50-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk51-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk52-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk53-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk54-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk55-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk56-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk57-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk58-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk59-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk60-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk61-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk62-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk63-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk64-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk65-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk66-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk67-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk68-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk69-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk70-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk71-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk72-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk73-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk74-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk75-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk76-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk77-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk78-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk79-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk80-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk81-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk82-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk83-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk84-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk85-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk86-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk87-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk88-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk89-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk90-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk91-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk92-u3049cf66aa/files/invalid_shard.shard", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk93-u3049cf66aa/files/invalid_shard.shard" ], "valid_reads": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u3049cf61a2/files/valid.shard" ] }, "sample_assignment_metrics": null, "sample_barcodes": null, "sequencing_metrics": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "slfe_feature_reference": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3049cf619f/files/feature_reference.frf.bincode", "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "target_set_name": null }, "setup_chunks_outs": { "barcode_whitelists": [ "3M-february-2018_TRU" ], "chunks": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I1_001.fastq.gz", "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_I2_001.fastq.gz", "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1/Peak-004-1_S1_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "cellranger-SSB01-apo_rep1:0:1:GW240319000:5", "read_lengths": {}, "subsample_rate": null, "umi_extractor": { "translators": [ null ] } } ], "visium_hd_slide_name": null }, "target_outs": { "bait_fasta": null, "disable_target_umi_filter": true, "disable_targeted": true, "no_bam": false, "probe_set": null, "target_gene_indices": null, "target_panel": null, "target_panel_or_probe_set": null, "target_panel_summary": null, "target_set_name": null, "targeting_method": null } }, "id": "count_gw", "type": "COUNT_GEM_WELL_PROCESSOR", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "analysis": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "analysis_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis_csv", "cloupe_matrix_h5": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/PREPROCESS_MATRIX/fork0/join-u3049cfab4c/files/cloupe_matrix_h5.h5", "skip_tsne": false, "summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/summary.json" }, "id": "count_analyzer", "type": "AnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "crispr_analyzer", "type": "_CRISPR_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_analyzer", "type": "_ANTIBODY_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_analyzer", "type": "_ANTIBODY_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "targeted_analyzer", "type": "_TARGETED_ANALYZER", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "assign_tags_outs", "type": "AssignTagsOuts", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": false, "id": "disable_library_cloupe", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_cloupe", "type": "map\u003ccloupe\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_cas_types", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cas_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_cloupe_name", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": { "feature_reference": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/feature_reference.csv", "metrics_summary_csv": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_csv.csv", "metrics_summary_json": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_json.json", "web_summary": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/web_summary.html", "ws_data": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/ws_data.json" }, "id": "count_summary", "type": "SUMMARIZE_REPORTS", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/chnk0-u3049cfb161/files/cloupe.cloupe", "id": "cloupe", "type": "cloupe", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_histograms", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_histograms", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcode_rank_plots", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "jibes_biplot_histogram", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cmo_projection_plot", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.GENERATE_LIBRARY_PLOTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "APPEND_CELL_TYPES_CLOUPE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.APPEND_CELL_TYPES_CLOUPE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cas_cell_typing/append_cell_types_cloupe", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/join-u3049cfb157/files/output_for_cloupe.cloupe", "id": "sample_cloupe", "type": "cloupe", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_cas_types", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cas_track_name", "type": "string", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.APPEND_CELL_TYPES_CLOUPE", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE/fork0/chnk0-u3049cfb161/files/cell_annotation_sample_cloupe.cloupe", "id": "cell_annotation_sample_cloupe", "type": "cloupe", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.APPEND_CELL_TYPES_CLOUPE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.APPEND_CELL_TYPES_CLOUPE" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "CHOOSE_CLOUPE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/choose_cloupe", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.APPEND_CELL_TYPES_CLOUPE", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/APPEND_CELL_TYPES_CLOUPE/fork0/chnk0-u3049cfb161/files/cell_annotation_sample_cloupe.cloupe", "id": "library_cloupe", "type": "cloupe", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_cloupe", "type": "map\u003ccloupe\u003e", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/chnk0-u3049cfb161/files/cloupe.cloupe", "id": "cloupe", "type": "cloupe", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CHOOSE_CLOUPE/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.APPEND_CELL_TYPES_CLOUPE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CHOOSE_CLOUPE" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "CLOUPE_PREPROCESS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/cloupe/cloupe_preprocess", "forks": [ { "argPermute": null, "joinDef": { "__threads": 2, "__mem_gb": 4, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "SC_RNA_COUNTER_CS", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_gene_bc_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_json.json", "id": "metrics_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "aggregation_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "gem_group_index_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "image_page_names", "type": "string[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_image_paths", "type": "file[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "dark_images", "type": "int", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_positions", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "fiducial_positions_list", "type": "txt", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "dzi_info", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "dzi_tiles_paths", "type": "path[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "scale_factors_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcode_whitelist", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "hd_slide_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "loupe_map", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "sc", "id": "product_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_sample", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_protospacer", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "spatial_enrichment", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "spatial_deconvolution_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "disable_cloupe", "type": "bool", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/join-u3049cfb157/files/output_for_cloupe.cloupe", "id": "output_for_cloupe", "type": "cloupe", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/CLOUPE_PREPROCESS/fork0/join-u3049cfb157/files/gem_group_index_json.json", "id": "gem_group_index_json", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.CLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "GENERATE_LIBRARY_PLOTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.GENERATE_LIBRARY_PLOTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/GENERATE_LIBRARY_PLOTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/GENERATE_LIBRARY_PLOTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/generate_library_plots", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/GENERATE_LIBRARY_PLOTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/GENERATE_LIBRARY_PLOTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/GENERATE_LIBRARY_PLOTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_count", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_assigner_pickle", "type": "pickle", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_tag", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "non_singlet_barcodes", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_STAGES", "matchedFork": null, "value": null, "id": "force_sample_barcodes", "type": "BarcodeAssignments", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multiplexing_method", "type": "string", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.GENERATE_LIBRARY_PLOTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.GENERATE_LIBRARY_PLOTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.GENERATE_LIBRARY_PLOTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.GENERATE_LIBRARY_PLOTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SUMMARIZE_REPORTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/counter/summarize_reports", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": [ "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3049cfb09e/files/summary.json", "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/summary.json", null, null, null, null ], "id": "summaries", "type": "json[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3049cfb12c/files/analysis", "id": "analysis", "type": "path", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_matrices_h5.h5", "id": "filtered_gene_bc_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.FILTER_BARCODES", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3049cf9433/files/filtered_barcodes.csv", "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_histograms", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_treemap", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_histograms", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_treemap", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_feature_metrics_csv", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "include_introns", "type": "bool", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_json.json", "id": "metrics_summary_json", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_csv.csv", "id": "metrics_summary_csv", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/web_summary.html", "id": "web_summary", "type": "html", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/feature_reference.csv", "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/ws_data.json", "id": "ws_data", "type": "json", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_SERVICE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.COUNT_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "MULTI_WEBSUMMARY_BUILDER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_WEBSUMMARY_BUILDER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t", "type": "map\u003cvwc.json\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd", "type": "map\u003cvwc.json\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b", "type": "map\u003cvwc.json\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "per_sample_metrics", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER.SUMMARIZE_REPORTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_REPORTER/SUMMARIZE_REPORTS/fork0/join-u3049cfb12f/files/metrics_summary_json.json", "id": "library_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_config", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_inputs", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "aligner": null, "annotations": null, "cell_annotation_model": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "chemistry_specs": { "Gene Expression": "auto" }, "custom_chemistry_def": null, "enable_tsne": true, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "genetic_demux_params": null, "include_exons": true, "include_introns": true, "initial_reads": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_secondary_analysis": false, "no_target_umi_filter": false, "primer_initial_reads": null, "primers": [ { "name": "P5", "seq": "AATGATACGGCGACCACCGAGATCT" }, { "name": "P7", "seq": "CAAGCAGAAGACGGCATACGAGAT" }, { "name": "R1", "seq": "ACACTCTTTCCCTACACGACG" }, { "name": "R2", "seq": "GTGACTGGAGTTCAGACGTGTG" }, { "name": "switch_oligo", "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG" }, { "name": "polyA", "seq": "AAAAAAAAAAAAAAAAAAAA" } ], "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "skip_cell_annotation": true, "special_genomic_regions": null, "subsample_rate": null, "target_set": null, "target_set_name": null, "targeting_method": null, "tenx_cloud_token_path": null, "tenx_cmos": null, "throughput": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "count_inputs", "type": "CountInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_gen_inputs", "type": "VdjGenInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u3049cf619f/files/sequencing_metrics.smf.json", "id": "sequencing_metrics", "type": "smf.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tag_contaminant_info", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_projection_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_barcode_rank_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_treemap_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "barcode_rank_plots", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antibody_histograms", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_barcharts", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_box_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_umap_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_diffexp_tables", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED", "matchedFork": null, "value": {}, "id": "cell_annotation_viable_but_not_requested", "type": "map\u003cbool\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_metrics_jsons", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_antibody_histograms", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_histograms", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "jibes_biplot_histogram", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cmo_projection_plot", "type": "json", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_set_name", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_vdj_metrics", "type": "map\u003cag.vdj.bincode\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "antigen_specificity", "type": "map\u003ccsv\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_config", "type": "FeatureConfig", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": { "Gene Expression": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": { "name": "3M-february-2018_TRU", "part": null, "slide": null, "translation": false, "translation_whitelist_path": null } } ], "barcode_extraction": null, "description": "Single Cell 3' v3 (polyA)", "endedness": "three_prime", "name": "SC3Pv3-polyA", "rna": { "length": null, "min_length": null, "offset": 0, "read_type": "R2" }, "rna2": null, "strandedness": "+", "umi": [ { "length": 12, "min_length": 10, "offset": 16, "read_type": "R1", "whitelist": null } ] } }, "id": "chemistry_defs", "type": "map\u003cChemistryDef\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY", "matchedFork": null, "value": null, "id": "detected_probe_barcode_pairing", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_preflight", "type": "bool", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CELL_ANNOTATION_VIABLE_BUT_NOT_REQUESTED", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.PICK_BEAM_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_WEBSUMMARY_BUILDER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "PICK_BEAM_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.PICK_BEAM_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/PICK_BEAM_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/PICK_BEAM_ANALYZER", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian pick_beam_analyzer", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/PICK_BEAM_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/PICK_BEAM_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/PICK_BEAM_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t", "type": "map\u003cBeamAnalyzerOutputs\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_t_gd", "type": "map\u003cBeamAnalyzerOutputs\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_b", "type": "map\u003cBeamAnalyzerOutputs\u003e", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.PICK_BEAM_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.PICK_BEAM_ANALYZER" } ], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "SAMPLE_ANALYZER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_ANALYZER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_ANALYZER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_ANALYZER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_ANALYZER", "mode": "map", "split": {} }, "id": "filtered_matrices_h5", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_ANALYZER", "mode": "map", "split": {} }, "id": "molecule_info", "type": "h5", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX", "matchedFork": null, "value": { "aligner": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "custom_chemistry_def": null, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "include_exons": true, "include_introns": true, "initial_reads": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_target_umi_filter": false, "primers": [ { "name": "P5", "seq": "AATGATACGGCGACCACCGAGATCT" }, { "name": "P7", "seq": "CAAGCAGAAGACGGCATACGAGAT" }, { "name": "R1", "seq": "ACACTCTTTCCCTACACGACG" }, { "name": "R2", "seq": "GTGACTGGAGTTCAGACGTGTG" }, { "name": "switch_oligo", "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG" }, { "name": "polyA", "seq": "AAAAAAAAAAAAAAAAAAAA" } ], "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "subsample_rate": null, "target_set": null, "target_set_name": null, "targeting_method": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "count_inputs", "type": "CounterInputs", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_ANALYZER", "mode": "map", "split": {} }, "id": "filtered_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_ANALYZER", "mode": "map", "split": {} }, "id": "aggregate_barcodes", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_ANALYZER", "mode": "map", "split": {} }, "id": "counter_metrics_json", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "disable_rna", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_crispr", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_antibody", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_antigen", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "matchedFork": null, "value": true, "id": "disable_targeted", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "no_secondary_analysis", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": { "bait_fasta": null, "disable_target_umi_filter": true, "disable_targeted": true, "no_bam": false, "probe_set": null, "target_gene_indices": null, "target_panel": null, "target_panel_or_probe_set": null, "target_panel_summary": null, "target_set_name": null, "targeting_method": null }, "id": "parse_target_features", "type": "PARSE_TARGET_FEATURES", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": true, "id": "enable_tsne", "type": "bool", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_ANALYZER", "mode": "map", "split": {} }, "id": "sample_id", "type": "string", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_FEATURE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "SAMPLE_CELL_ANNOTATION_SERVICE", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_CELL_ANNOTATION_SERVICE", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_CELL_ANNOTATION_SERVICE", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_CELL_ANNOTATION_SERVICE/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_CELL_ANNOTATION_SERVICE/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_CELL_ANNOTATION_SERVICE/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_CELL_ANNOTATION_SERVICE", "mode": "map", "split": {} }, "id": "filtered_matrix", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "call": "SAMPLE_CELL_ANNOTATION_SERVICE", "mode": "map", "split": null }, "id": "analysis", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_CELL_ANNOTATION_SERVICE", "mode": "map", "split": {} }, "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_positions", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tissue_lowres_image", "type": "png", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "scale_factors", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cell_annotation_model", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "tenx_cloud_token_path", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_MULTI_CORE_SAMPLE", "id": "pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "alert_string", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": false, "id": "is_pd", "type": "bool", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cloupe_projection", "type": "csv", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_cloupe", "type": "cloupe", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.DISABLE_MULTI_CORE_STAGES", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "SAMPLE_REPORTER", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_REPORTER", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_REPORTER", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_REPORTER/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_REPORTER/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SAMPLE_REPORTER/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": { "call": "SAMPLE_REPORTER", "mode": "map", "split": {} }, "id": "sample_outs", "type": "SampleSlfeOuts", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "call": "SAMPLE_REPORTER", "mode": "map", "split": null }, "id": "count_analyzer", "type": "AnalyzerOutputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "call": "SAMPLE_REPORTER", "mode": "map", "split": null }, "id": "crispr_analyzer", "type": "_CRISPR_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "call": "SAMPLE_REPORTER", "mode": "map", "split": null }, "id": "targeted_analyzer", "type": "_TARGETED_ANALYZER", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "call": "SAMPLE_REPORTER", "mode": "map", "split": null }, "id": "sample_assignment_metrics", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "call": "SAMPLE_REPORTER", "mode": "map", "split": null }, "id": "cloupe_cas_types", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "call": "SAMPLE_REPORTER", "mode": "map", "split": null }, "id": "cell_annotation_cloupe_name", "type": "string", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel_summary", "type": "tps.json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "cellranger-SSB01-apo_rep1", "id": "sample_id", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SSB01-apo_rep1", "id": "sample_desc", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_vdj_b": true, "disable_vdj_t": true, "disable_vdj_t_gd": true, "has_no_vdj_ref": true }, "id": "config", "type": "FullPipelineConfig", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "SC_RNA_COUNTER_CS", "id": "count_pipestance_type", "type": "string", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "id": "cell_calling_config", "type": "CellCalling", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u3049cf942a/files/barcode_summary.h5", "id": "barcode_summary", "type": "h5", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_sample", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "cells_per_tag", "type": "json", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_ANALYZER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_CELL_ANNOTATION_SERVICE", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER" } ], "stagecodeLang": "", "type": "pipeline" }, { "name": "SANITIZE_MAP_CALLS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/sanitize_map_calls", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SANITIZE_MAP_CALLS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_crispr_analysis", "type": "map\u003cpath\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_rna_analysis", "type": "map\u003cpath\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_cloupe_file", "type": "map\u003ccloupe\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_metrics_summary", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_sample_projection_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_sample_barcode_rank_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_sample_treemap_plots", "type": "map\u003cjson\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_vdj_t_analyzer", "type": "map\u003cVDJ_ANALYZER\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_vdj_t_gd_analyzer", "type": "map\u003cVDJ_ANALYZER\u003e", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "in_vdj_b_analyzer", "type": "map\u003cVDJ_ANALYZER\u003e", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SAMPLE_REPORTER", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "SPLIT_VDJ_INPUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SPLIT_VDJ_INPUTS", "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SPLIT_VDJ_INPUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/vdj/split_vdj_inputs", "forks": [ { "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SPLIT_VDJ_INPUTS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SPLIT_VDJ_INPUTS/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/SPLIT_VDJ_INPUTS/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": [], "id": "vdj_inputs", "type": "VdjInputs[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_chemistry_defs", "type": "ChemistryDef[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "vdj_receptors", "type": "string[]", "waiting": false } ], "Return": null }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SPLIT_VDJ_INPUTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "STRUCTIFY_PER_SAMPLE_OUTS", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/mro/rna/stages/multi/structify_per_sample_outs", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_bams", "type": "SampleBamFile[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_metrics", "type": "SampleMetrics[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_molecule_infos", "type": "SampleMoleculeInfo[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "sample_matrices", "type": "SampleMatrices[]", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "multi_graph", "type": "json", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": null, "id": "feature_reference", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "target_panel", "type": "csv", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES", "matchedFork": null, "value": null, "id": "probe_set", "type": "csv", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": {}, "id": "sample_outs", "type": "map\u003cSampleSlfeOuts\u003e", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-u3049cfab49/files/unassigned_alignments.bam", "id": "unassigned_alignments", "type": "bam", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-u3049cfab49/files/unassigned_alignments_bai_index.bam.bai", "id": "unassigned_alignments_bai_index", "type": "bam.bai", "waiting": false }, { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0-u3049cfab49/files/unassigned_alignments_csi_index.bam.csi", "id": "unassigned_alignments_csi_index", "type": "bam.csi", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/STRUCTIFY_PER_SAMPLE_OUTS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.CREATE_MULTI_GRAPH", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.SC_MULTI_CORE.STRUCTIFY_PER_SAMPLE_OUTS" } ], "stagecodeLang": "Python", "type": "stage" }, { "name": "WRITE_GENE_INDEX", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX", "names": [] }, "stagecodeCmd": "/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/bin/cr_lib martian write_gene_index", "forks": [ { "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 6, "__vmem_gb": 9 }, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "id": "reference_path", "type": "path", "waiting": false } ], "Return": [ { "mode": "reference", "node": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX", "matchedFork": null, "value": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "id": "gene_index", "type": "json", "waiting": false } ] }, "chunks": [ { "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9 }, "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "state": "complete", "index": 0 } ], "index": 0 } ], "edges": [], "stagecodeLang": "Compiled", "type": "stage" }, { "name": "_STRUCTIFY", "fqname": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY", "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/_STRUCTIFY", "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/_STRUCTIFY", "names": [] }, "stagecodeCmd": "", "forks": [ { "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/_STRUCTIFY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/_STRUCTIFY/fork0/split", "names": [] }, "join_metadata": { "path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/_STRUCTIFY/fork0/join", "names": [] }, "bindings": { "Argument": [ { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "aligner": null, "cell_annotation_model": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "chemistry_specs": { "Gene Expression": "auto" }, "emptydrops_minimum_umis": null, "enable_tsne": true, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "global_minimum_umis": null, "include_introns": true, "max_mito_percent": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_secondary_analysis": false, "no_target_umi_filter": false, "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "skip_cell_annotation": true, "target_set": null, "target_set_name": null, "targeting_method": null, "tenx_cloud_token_path": null, "tenx_cmos": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "count_input", "type": "CountInputsCS", "waiting": false } ], "Return": [ { "mode": "", "node": null, "matchedFork": null, "value": { "multi_config_sha": null, "sample_desc": "SSB01-apo_rep1", "sample_id": "cellranger-SSB01-apo_rep1" }, "id": "common_input", "type": "CommonInputs", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "aligner": null, "cell_annotation_model": null, "cell_calling_config": { "cell_barcodes": null, "disable_ab_aggregate_detection": false, "disable_high_occupancy_gem_detection": false, "emptydrops_minimum_umis": { "per_gem_well": null, "per_sample": null }, "force_cells": { "per_gem_well": null, "per_sample": null }, "global_minimum_umis": { "per_gem_well": null, "per_sample": null }, "max_mito_percent": { "per_gem_well": null, "per_sample": null }, "override_library_types": null, "override_mode": null, "recovered_cells": { "per_gem_well": null, "per_sample": null } }, "check_library_compatibility": true, "chemistry_specs": { "Gene Expression": "auto" }, "emptydrops_minimum_umis": null, "enable_tsne": true, "feature_reference": null, "filter_probes": null, "force_sample_barcodes": { "cells_per_tag": null, "non_singlet_barcodes": null, "sample_barcodes": null }, "gene_index": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-SSB01-apo_rep1/SC_RNA_COUNTER_CS/WRITE_GENE_INDEX/fork0/chnk0-u3049cf6185/files/gene_index.json", "global_minimum_umis": null, "include_introns": true, "max_mito_percent": null, "min_assignment_confidence": null, "min_crispr_umi_threshold": 3, "no_bam": false, "no_secondary_analysis": false, "no_target_umi_filter": false, "r1_length": null, "r2_length": null, "reference_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Symbiodinium_minutum_Clade_B1_Ver1_120123", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/apo_rep1", "sample_indices": [ "any" ], "sample_names": [ "Peak-004-1" ], "subsample_rate": null } ], "skip_cell_annotation": true, "target_set": null, "target_set_name": null, "targeting_method": null, "tenx_cloud_token_path": null, "tenx_cmos": null, "trim_polya_min_score": 20, "trim_tso_min_score": 20 }, "id": "count_input", "type": "CountInputsCS", "waiting": false }, { "mode": "", "node": null, "matchedFork": null, "value": { "disable_annotate": true, "disable_count": false, "disable_multi": true, "disable_multi_count": true, "disable_rtl": true, "disable_vdj": true }, "id": "config", "type": "BasicPipelineConfig", "waiting": false } ] }, "chunks": [], "index": 0 } ], "edges": [ { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY" }, { "from": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX", "to": "ID.cellranger-SSB01-apo_rep1.SC_RNA_COUNTER_CS._STRUCTIFY" } ], "stagecodeLang": "", "type": "pipeline" } ]