[ { "name": "SC_ATAC_GEX_COUNTER_CS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null }, { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "force_cells", "type": "map\u003cMinCounts\u003e", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "skip_compatibility_check", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "rna_include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "custom_peaks", "type": "bed", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "feature_linkage_max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "k_means_max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "no_bam", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false } ], "Return": [ { "id": "analysis", "type": "AnalysisOutput", "mode": "", "node": null, "matchedFork": null, "value": { "clustering": { "atac": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } }, "gex": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } } }, "dimensionality_reduction": { "atac": { "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/projection.csv", "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/components.csv", "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv", "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/variance.csv", "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_umap_csv/2_components/projection.csv" }, "gex": { "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "pca_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/components.csv", "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/dispersion.csv", "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/variance.csv", "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_umap_csv/2_components/projection.csv" } }, "feature_linkage": { "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage.bedpe", "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage_matrix.h5" }, "tf_analysis": { "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix_mex", "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u9761b6d667/files/peak_motif_hits.bed" } }, "waiting": false }, { "id": "web_summary", "type": "html", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-u9761b6d7fb/files/web_summary.html", "waiting": false }, { "id": "summary", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/summary_csv_cs.csv", "waiting": false }, { "id": "per_barcode_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/metrics_cs.csv", "waiting": false }, { "id": "filtered_feature_bc_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_filtered_matrix_mex", "waiting": false }, { "id": "filtered_feature_bc_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5", "waiting": false }, { "id": "raw_feature_bc_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix_mex", "waiting": false }, { "id": "raw_feature_bc_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix.h5", "waiting": false }, { "id": "cloupe", "type": "cloupe", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u9761b6d7fb/files/output_for_cloupe.cloupe", "waiting": false }, { "id": "gex_possorted_bam", "type": "bam", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-u9761b6d4fd/files/pos_sorted_non_multiplexed.bam", "waiting": false }, { "id": "gex_possorted_bam_index", "type": "bam.bai", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-u9761b6d4fd/files/pos_sorted_non_multiplexed.bam.bai", "waiting": false }, { "id": "gex_molecule_info", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u9761b6d563/files/molecule_info_non_multiplexed.h5", "waiting": false }, { "id": "atac_possorted_bam", "type": "bam", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam", "waiting": false }, { "id": "atac_possorted_bam_index", "type": "bam.bai", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam.bai", "waiting": false }, { "id": "atac_fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "atac_fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "atac_peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "atac_cut_sites", "type": "bigwig", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-u9761b6d137/files/cut_sites.bigwig", "waiting": false }, { "id": "atac_peak_annotation", "type": "tsv", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ARC_COUNTER_PREFLIGHT_LOCAL", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.ARC_COUNTER_PREFLIGHT_LOCAL", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/ARC_COUNTER_PREFLIGHT_LOCAL/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "on_cluster", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "force_cells", "type": "map\u003cMinCounts\u003e", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null }, { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "feature_linkage_max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "k_means_max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_r1_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_r2_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_custom_peaks", "type": "bed", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": null } } ], "edges": [], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/preflight/arc_counter_preflight" }, { "name": "SC_ATAC_GEX_COUNTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null }, { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "force_cells", "type": "map\u003cMinCounts\u003e", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "skip_compatibility_check", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "feature_linkage_max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "k_means_max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "no_bam", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "rna_chemistry", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "ARC-v1", "waiting": false }, { "id": "rna_custom_chemistry_def", "type": "ChemistryDef", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_recovered_cells", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1000, "waiting": false }, { "id": "rna_subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "rna_initial_reads", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_r1_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_r2_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_feature_reference", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "rna_trim_polya_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "rna_trim_tso_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "atac_subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_barcode_whitelist", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "atac_custom_peaks", "type": "bed", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "disable_bc_multiplets", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false } ], "Return": [ { "id": "web_summary", "type": "AnalysisHTML", "mode": "", "node": null, "matchedFork": null, "value": { "atac": null, "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-u9761b6d7fb/files/web_summary.html", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/web_summary.html" }, "waiting": false }, { "id": "summary_csv", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/summary_csv_cs.csv", "waiting": false }, { "id": "per_barcode_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/metrics.csv", "waiting": false }, { "id": "per_barcode_metrics_cs", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/metrics_cs.csv", "waiting": false }, { "id": "filtered_feature_bc_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_filtered_matrix_mex", "waiting": false }, { "id": "filtered_feature_bc_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5", "waiting": false }, { "id": "raw_feature_bc_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix_mex", "waiting": false }, { "id": "raw_feature_bc_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix.h5", "waiting": false }, { "id": "analysis", "type": "AnalysisOutput", "mode": "", "node": null, "matchedFork": null, "value": { "clustering": { "atac": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } }, "gex": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } } }, "dimensionality_reduction": { "atac": { "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/projection.csv", "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/components.csv", "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv", "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/variance.csv", "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_umap_csv/2_components/projection.csv" }, "gex": { "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "pca_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/components.csv", "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/dispersion.csv", "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/variance.csv", "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_umap_csv/2_components/projection.csv" } }, "feature_linkage": { "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage.bedpe", "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage_matrix.h5" }, "tf_analysis": { "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix_mex", "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u9761b6d667/files/peak_motif_hits.bed" } }, "waiting": false }, { "id": "cloupe", "type": "cloupe", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u9761b6d7fb/files/output_for_cloupe.cloupe", "waiting": false }, { "id": "gex_possorted_genome_bam", "type": "bam", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-u9761b6d4fd/files/pos_sorted_non_multiplexed.bam", "waiting": false }, { "id": "gex_possorted_genome_bam_index", "type": "bam.bai", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-u9761b6d4fd/files/pos_sorted_non_multiplexed.bam.bai", "waiting": false }, { "id": "gex_molecule_info", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u9761b6d563/files/molecule_info_non_multiplexed.h5", "waiting": false }, { "id": "atac_possorted_bam", "type": "bam", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam", "waiting": false }, { "id": "atac_possorted_bam_index", "type": "bam.bai", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam.bai", "waiting": false }, { "id": "atac_fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "atac_fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "atac_peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "atac_cut_sites", "type": "bigwig", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-u9761b6d137/files/cut_sites.bigwig", "waiting": false }, { "id": "atac_peak_annotation", "type": "tsv", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false }, { "id": "is_multi_genome", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "pd_gex_inputs", "type": "PdGEXInputs", "mode": "", "node": null, "matchedFork": null, "value": { "alignments": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/pos_sorted.asf" ], "annotation_files": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4" ], "barcode_summary_h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u9761b6d4fd/files/barcode_summary.h5", "barcode_whitelist": "737K-arc-v1", "filtered_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "filtered_gene_bc_matrices_h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "gem_groups": [ 1 ], "is_multi_genome": false, "per_barcode_metrics": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-u9761b6d563/files/augmented_metrics.csv", "raw_gene_bc_matrices_h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "read_shards": { "corrected_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/valid_shard.shard" ], "invalid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/invalid_shard.shard" ], "valid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/valid.shard" ] }, "summary": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/metrics_summary_json.json" }, "waiting": false }, { "id": "pd_atac_inputs", "type": "PdATACInputs", "mode": "", "node": null, "matchedFork": null, "value": { "basic_summary": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/summary.json", "bulk_complexity": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/bulk_complexity.json", "cell_calling_summary": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-u9761b6d563/files/merged_summary.json", "complexity_summary": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/complexity_summary.json", "count_dict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/count_dict.json", "ctcf_relpos": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/ctcf.csv", "enrichment_results": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-u9761b6d53a/files/summary_metrics.json", "excluded_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u9761b6d527/files/excluded_barcodes.json", "filtered_peak_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "insert_summary": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-u9761b6d0e6/files/insert_summary.json", "peak_summary": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peak_metrics.json", "sample_def": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "sc_insert_sizes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/insert_sizes.csv", "singlecell": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5ec/files/singlecell.csv", "singlecell_complexity": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/singlecell_complexity.json", "singlecell_results": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5fd/files/summary.json", "tss_relpos": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/tss.csv" }, "waiting": false }, { "id": "analysis_h5", "type": "h5", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u9761b6d784/files/analysis_h5.h5", "waiting": false }, { "id": "analysis_summary", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ARC_COUNTER_PREFLIGHT", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ARC_COUNTER_PREFLIGHT", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ARC_COUNTER_PREFLIGHT/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "on_cluster", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "force_cells", "type": "map\u003cMinCounts\u003e", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null }, { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "feature_linkage_max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "k_means_max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_r1_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_r2_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_custom_peaks", "type": "bed", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": null } } ], "edges": [], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/preflight/arc_counter_preflight" }, { "name": "ATAC_GEX_CLOUPE_PREPROCESS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8.697265625, "__vmem_gb": 11.697265625 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "pipestance_type", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "SC_ATAC_GEX_COUNTER", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "analysis", "type": "h5", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u9761b6d784/files/analysis_h5.h5", "waiting": false }, { "id": "feature_barcode_matrix", "type": "h5", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u9761b6d784/files/loupe_matrix_h5.h5", "waiting": false }, { "id": "metrics_json", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/summary.json", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "aggregation_csv", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "gem_group_index_json", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "no_secondary_analysis", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false } ], "Return": [ { "id": "output_for_cloupe", "type": "cloupe", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/ATAC_GEX_CLOUPE_PREPROCESS/fork0/join-u9761b6d7fb/files/output_for_cloupe.cloupe", "waiting": false }, { "id": "gem_group_index_json", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS", "matchedFork": null, "value": null, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.ATAC_GEX_CLOUPE_PREPROCESS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/cloupe/atac_cloupe_preprocess" }, { "name": "CHECK_JOINT_BARCODES_COMPATIBILITY", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CHECK_JOINT_BARCODES_COMPATIBILITY", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CHECK_JOINT_BARCODES_COMPATIBILITY/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "atac_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u9761b69f69/files/barcode_counts.json", "waiting": false }, { "id": "gex_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/bc_counts_json.json", "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "737K-arc-v1", "waiting": false } ], "Return": null } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CHECK_JOINT_BARCODES_COMPATIBILITY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CHECK_JOINT_BARCODES_COMPATIBILITY" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/check_joint_barcodes_compatibility" }, { "name": "COMPILE_GEX_BARCODE_METRICS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/per_barcode_metrics.csv", "waiting": false }, { "id": "filtered_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false } ], "Return": [ { "id": "augmented_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-u9761b6d563/files/augmented_metrics.csv", "waiting": false }, { "id": "wasted_data_metrics", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-u9761b6d563/files/wasted_data_metrics.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/reporter/compile_gex_barcode_metrics" }, { "name": "CREATE_JOINT_WEBSUMMARY", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 16, "__vmem_gb": 19 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 16, "__threads": 1, "__vmem_gb": 19 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/summary.json", "waiting": false }, { "id": "merge_singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/metrics.csv", "waiting": false }, { "id": "analysis_csv", "type": "AnalysisOutput", "mode": "", "node": null, "matchedFork": null, "value": { "clustering": { "atac": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } }, "gex": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } } }, "dimensionality_reduction": { "atac": { "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/projection.csv", "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/components.csv", "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv", "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/variance.csv", "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_umap_csv/2_components/projection.csv" }, "gex": { "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "pca_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/components.csv", "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/dispersion.csv", "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/variance.csv", "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_umap_csv/2_components/projection.csv" } }, "feature_linkage": { "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage.bedpe", "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage_matrix.h5" }, "tf_analysis": { "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix_mex", "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u9761b6d667/files/peak_motif_hits.bed" } }, "waiting": false }, { "id": "atac_data", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-u9761b6d77a/files/data.json", "waiting": false }, { "id": "gex_data", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/ws_data.json", "waiting": false }, { "id": "debug", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "rna_include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "atac_peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "feature_linkage_max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "web_summary", "type": "html", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-u9761b6d7fb/files/web_summary.html", "waiting": false }, { "id": "data", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/CREATE_JOINT_WEBSUMMARY/fork0/chnk0-u9761b6d7fb/files/data.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.CREATE_JOINT_WEBSUMMARY" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/reporter/create_joint_websummary" }, { "name": "GEX_SUMMARIZE_REPORTS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "summaries", "type": "json[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u9761b6d7a5/files/summary.json" ], "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "analysis", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "barcode_summary_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u9761b6d4fd/files/barcode_summary.h5", "waiting": false }, { "id": "filtered_gene_bc_matrices_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "filtered_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "gem_groups", "type": "int[]", "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "waiting": false }, { "id": "feature_reference", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_set_name", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "per_feature_metrics_csv", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false } ], "Return": [ { "id": "metrics_summary_json", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/metrics_summary_json.json", "waiting": false }, { "id": "metrics_summary_csv", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/metrics_summary_csv.csv", "waiting": false }, { "id": "web_summary", "type": "html", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/web_summary.html", "waiting": false }, { "id": "feature_reference", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/feature_reference.csv", "waiting": false }, { "id": "ws_data", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/ws_data.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/counter/summarize_reports" }, { "name": "MERGE_RNA_ATAC_DATA", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "disable_atac", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "disable_rna", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "atac_summary_csv_cs", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/summary_csv.csv", "waiting": false }, { "id": "rna_summary_csv_cs", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/metrics_summary_csv.csv", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "atac_whitelist", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "rna_whitelist", "type": "string", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "atac_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5ec/files/singlecell.csv", "waiting": false }, { "id": "rna_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-u9761b6d563/files/augmented_metrics.csv", "waiting": false }, { "id": "joint_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/singlecell.csv", "waiting": false }, { "id": "atac_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix.h5", "waiting": false }, { "id": "rna_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "filtered_atac_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "filtered_rna_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "rna_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u9761b6d7b1/files/metrics_summary_json.json", "waiting": false }, { "id": "atac_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/summary.json", "waiting": false }, { "id": "joint_summaries", "type": "json[]", "mode": "", "node": null, "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-u9761b6d563/files/merged_summary.json", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/summary.json" ], "waiting": false } ], "Return": [ { "id": "metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/metrics.csv", "waiting": false }, { "id": "metrics_cs", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/metrics_cs.csv", "waiting": false }, { "id": "metrics_cells_only", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/metrics_cells_only.csv", "waiting": false }, { "id": "matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/matrix.h5", "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/summary.json", "waiting": false }, { "id": "summary_csv_cs", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u9761b6d7b5/files/summary_csv_cs.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.COMPILE_GEX_BARCODE_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.GEX_SUMMARIZE_REPORTS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.MERGE_RNA_ATAC_DATA" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/merge_rna_atac_data" }, { "name": "SPLIT_SAMPLE_DEF", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/SPLIT_SAMPLE_DEF/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "sample_def", "type": "map[]", "mode": "", "node": null, "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null }, { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false } ], "Return": [ { "id": "atac_sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "rna_sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false } ] } } ], "edges": [], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/split_sample_def" }, { "name": "WRITE_POS_BAM", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 4, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 0, 192537976, 8837270183615663993, 1412810544, 0 ], "start": null }, "write_header": true }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 2, 6500135, 7201322664114368084, 2234466623, 16 ], "start": [ 0, 192537976, 8837270183615663993, 1412810544, 0 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 3, 46193155, 12958710095605376273, 2411687570, 1040 ], "start": [ 2, 6500135, 7201322664114368084, 2234466623, 16 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 5, 69438963, 765946979222262570, 2411687570, 1024 ], "start": [ 3, 46193155, 12958710095605376273, 2411687570, 1040 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 7, 89285401, 2789283944863516992, 2411687570, 1040 ], "start": [ 5, 69438963, 765946979222262570, 2411687570, 1024 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 9, 74836134, 17923200002683671469, 2411687570, 16 ], "start": [ 7, 89285401, 2789283944863516992, 2411687570, 1040 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 11, 68257044, 15183249741523072614, 2411687570, 0 ], "start": [ 9, 74836134, 17923200002683671469, 2411687570, 16 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 12, 60367977, 13731655314988992092, 2411687570, 1024 ], "start": [ 11, 68257044, 15183249741523072614, 2411687570, 0 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 15, 112447028, 11996341653404422375, 2411687570, 0 ], "start": [ 12, 60367977, 13731655314988992092, 2411687570, 1024 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 16, 177601281, 3568648806152685938, 2411687570, 0 ], "start": [ 15, 112447028, 11996341653404422375, 2411687570, 0 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 18, 5416829, 13702478501113409632, 2411687570, 0 ], "start": [ 16, 177601281, 3568648806152685938, 2411687570, 0 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 19, 22954907, 7423079333048889607, 1247225523, 16 ], "start": [ 18, 5416829, 13702478501113409632, 2411687570, 0 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 20, 98623640, 8809814092963885826, 2465834405, 16 ], "start": [ 19, 22954907, 7423079333048889607, 1247225523, 16 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": [ 23, 119581818, 11743187237571904044, 2411687570, 1024 ], "start": [ 20, 98623640, 8809814092963885826, 2465834405, 16 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 2, "__threads": 2, "__vmem_gb": 5, "range": { "end": null, "start": [ 23, 119581818, 11743187237571904044, 2411687570, 1024 ] }, "write_header": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "target_set_name", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "read_chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "sample_barcodes_json", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "no_bam", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "bam_header", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u9761b6bfc5/files/bam_header", "waiting": false }, { "id": "alignments", "type": "asf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/pos_sorted.asf" ], "waiting": false } ], "Return": [ { "id": "pos_sorted_bam", "type": "SampleBamFile", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "matchedFork": null, "value": { "bam_file": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-u9761b6d4fd/files/pos_sorted_non_multiplexed.bam", "bam_index_file": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/WRITE_POS_BAM/fork0/join-u9761b6d4fd/files/pos_sorted_non_multiplexed.bam.bai", "sample": "non_multiplexed" }, "waiting": false }, { "id": "multi_pos_sorted_bam", "type": "SampleBamFile[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM", "matchedFork": null, "value": null, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.WRITE_POS_BAM" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_pos_bam" }, { "name": "_ATAC_MATRIX_COMPUTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "chunks", "type": "FastqDef[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": [ { "read1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R1_001.fastq.gz", "read2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R3_001.fastq.gz", "reads_interleaved": false, "barcode": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R2_001.fastq.gz", "sample_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_I1_001.fastq.gz", "gem_group": 1, "subsample_rate": 1.0, "read_group": "samp24_CR_out:MissingLibrary:1:H5CK3DSX2:2", "chemistry": null, "fastq_mode": "ILMN_BCL2FASTQ" } ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_whitelist_path", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz", "waiting": false }, { "id": "custom_peaks", "type": "bed", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "no_bam", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "assay", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "arc", "waiting": false } ], "Return": [ { "id": "possorted_bam", "type": "bam", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam", "waiting": false }, { "id": "possorted_bam_index", "type": "bam.bai", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam.bai", "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "cut_sites", "type": "bigwig", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-u9761b6d137/files/cut_sites.bigwig", "waiting": false }, { "id": "count_dict", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/count_dict.json", "waiting": false }, { "id": "singlecell_mapping", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/singlecell.csv", "waiting": false }, { "id": "peak_metrics", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peak_metrics.json", "waiting": false }, { "id": "raw_peak_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix.h5", "waiting": false }, { "id": "raw_peak_bc_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix_mex", "waiting": false }, { "id": "insert_sizes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/insert_sizes.csv", "waiting": false }, { "id": "basic_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/summary.json", "waiting": false }, { "id": "bc_counts_json", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u9761b69f69/files/barcode_counts.json", "waiting": false }, { "id": "frag_bc_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/frag_bc_counts.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ALIGN_ATAC_READS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 9850368, "start": null } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 19692288, "start": 9850368 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 29542400, "start": 19692288 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 39384320, "start": 29542400 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 49234688, "start": 39384320 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 59084800, "start": 49234688 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 68926720, "start": 59084800 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 78776832, "start": 68926720 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 88618752, "start": 78776832 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 98469120, "start": 88618752 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 108319232, "start": 98469120 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 118161152, "start": 108319232 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 128011264, "start": 118161152 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 137853184, "start": 128011264 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 147703552, "start": 137853184 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 157553664, "start": 147703552 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 167395584, "start": 157553664 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 177245696, "start": 167395584 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 187087616, "start": 177245696 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 196937984, "start": 187087616 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 206788096, "start": 196937984 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 216630016, "start": 206788096 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 226480128, "start": 216630016 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 236322304, "start": 226480128 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 246172416, "start": 236322304 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 256022528, "start": 246172416 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 265864448, "start": 256022528 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 275714560, "start": 265864448 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": 285556736, "start": 275714560 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 12, "__threads": 4, "__vmem_gb": 15, "range": { "end": null, "start": 285556736 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0-u9761b69f69/files/out.shard" ], "waiting": false }, { "id": "chunk_chemistry_map", "type": "string[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": [ "3p;rev" ], "waiting": false }, { "id": "barcode_counts", "type": "bch.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u9761b69f69/files/barcode_counts.bch.bincode", "waiting": false }, { "id": "barcode_whitelist_path", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz", "waiting": false }, { "id": "chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": [ { "read1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R1_001.fastq.gz", "read2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R3_001.fastq.gz", "reads_interleaved": false, "barcode": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R2_001.fastq.gz", "sample_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_I1_001.fastq.gz", "gem_group": 1, "subsample_rate": 1.0, "read_group": "samp24_CR_out:MissingLibrary:1:H5CK3DSX2:2", "chemistry": null, "fastq_mode": "ILMN_BCL2FASTQ" } ], "waiting": false }, { "id": "num_read_pairs", "type": "int", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": 295403617, "waiting": false }, { "id": "assay", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "arc", "waiting": false } ], "Return": [ { "id": "aligned_shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-u9761b6a514/files/aligned_chunk.shard" ], "waiting": false }, { "id": "unaligned_shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-u9761b6a514/files/unaligned_chunk.shard" ], "waiting": false }, { "id": "stats", "type": "map", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS", "matchedFork": null, "value": { "footprint": { "denominator": 295403617, "numerator": 295099942 }, "high_mapq": { "denominator": 590807234, "numerator": 521668458 }, "num_read_pairs": 295403617, "valid_barcode": { "denominator": 295403617, "numerator": 292589412 } }, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian align_atac_reads" }, { "name": "GENERATE_PEAK_MATRIX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3.80078125, "__vmem_gb": 6.80078125 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_0.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_1.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_2.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_3.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_4.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_5.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_6.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_7.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_8.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_9.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_10.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_11.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_12.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_13.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_14.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_15.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_16.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_17.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_18.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_19.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_20.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_21.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_22.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_23.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_24.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_25.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_26.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_27.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_28.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 1.52, "__threads": 1, "__vmem_gb": 4.52, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/split-u9761b6d34b/files/barcode_29.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "frag_bc_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/frag_bc_counts.json", "waiting": false } ], "Return": [ { "id": "raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix.h5", "waiting": false }, { "id": "raw_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix_mex", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/generate_peak_matrix" }, { "name": "MAKE_ATAC_SHARDS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "chunk": { "barcode": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R2_001.fastq.gz", "chemistry": null, "gem_group": 1, "read1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R1_001.fastq.gz", "read2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R3_001.fastq.gz", "read_group": "samp24_CR_out:MissingLibrary:1:H5CK3DSX2:2", "reads_interleaved": false, "sample_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_I1_001.fastq.gz", "subsample_rate": 1.0 }, "chunk_id": 0 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": [ { "read1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R1_001.fastq.gz", "read2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R3_001.fastq.gz", "reads_interleaved": false, "barcode": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R2_001.fastq.gz", "sample_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_I1_001.fastq.gz", "gem_group": 1, "subsample_rate": 1.0, "read_group": "samp24_CR_out:MissingLibrary:1:H5CK3DSX2:2", "chemistry": null, "fastq_mode": "ILMN_BCL2FASTQ" } ], "waiting": false }, { "id": "barcode_whitelist_path", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz", "waiting": false } ], "Return": [ { "id": "shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0-u9761b69f69/files/out.shard" ], "waiting": false }, { "id": "chunk_chemistry_map", "type": "string[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": [ "3p;rev" ], "waiting": false }, { "id": "barcode_counts_json", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u9761b69f69/files/barcode_counts.json", "waiting": false }, { "id": "barcode_counts", "type": "bch.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u9761b69f69/files/barcode_counts.bch.bincode", "waiting": false }, { "id": "num_read_pairs", "type": "int", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": 295403617, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian make_atac_shards" }, { "name": "MARK_ATAC_DUPLICATES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 3, "__mem_gb": 7, "__vmem_gb": 10 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 9924988135004907095, "five_p": { "contig_id": 0, "pos": 57423320 }, "three_p": { "contig_id": 0, "pos": 57423941 } }, "start": null }, "unaligned_range": { "end": 9851010, "start": null } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 15033147975237402640, "five_p": { "contig_id": 0, "pos": 167342254 }, "three_p": { "contig_id": 0, "pos": 167342442 } }, "start": { "bc_hash": 9924988135004907095, "five_p": { "contig_id": 0, "pos": 57423320 }, "three_p": { "contig_id": 0, "pos": 57423941 } } }, "unaligned_range": { "end": 19694344, "start": 9851010 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 4581143959951978623, "five_p": { "contig_id": 1, "pos": 12781938 }, "three_p": { "contig_id": 1, "pos": 12782072 } }, "start": { "bc_hash": 15033147975237402640, "five_p": { "contig_id": 0, "pos": 167342254 }, "three_p": { "contig_id": 0, "pos": 167342442 } } }, "unaligned_range": { "end": 29543271, "start": 19694344 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk02", "names": [ "args", "complete", "heartbeat", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 10211525899225130262, "five_p": { "contig_id": 1, "pos": 106153222 }, "three_p": { "contig_id": 1, "pos": 106153670 } }, "start": { "bc_hash": 4581143959951978623, "five_p": { "contig_id": 1, "pos": 12781938 }, "three_p": { "contig_id": 1, "pos": 12782072 } } }, "unaligned_range": { "end": 39385545, "start": 29543271 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 556587828048203738, "five_p": { "contig_id": 2, "pos": 63294597 }, "three_p": { "contig_id": 2, "pos": 63294751 } }, "start": { "bc_hash": 10211525899225130262, "five_p": { "contig_id": 1, "pos": 106153222 }, "three_p": { "contig_id": 1, "pos": 106153670 } } }, "unaligned_range": { "end": 49235840, "start": 39385545 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 15308618405767789707, "five_p": { "contig_id": 3, "pos": 10212416 }, "three_p": { "contig_id": 3, "pos": 10212514 } }, "start": { "bc_hash": 556587828048203738, "five_p": { "contig_id": 2, "pos": 63294597 }, "three_p": { "contig_id": 2, "pos": 63294751 } } }, "unaligned_range": { "end": 59087235, "start": 49235840 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 8122031257852557793, "five_p": { "contig_id": 4, "pos": 31438857 }, "three_p": { "contig_id": 4, "pos": 31438857 } }, "start": { "bc_hash": 15308618405767789707, "five_p": { "contig_id": 3, "pos": 10212416 }, "three_p": { "contig_id": 3, "pos": 10212514 } } }, "unaligned_range": { "end": 68927386, "start": 59087235 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 12612432056225637305, "five_p": { "contig_id": 5, "pos": 60854485 }, "three_p": { "contig_id": 5, "pos": 60854924 } }, "start": { "bc_hash": 8122031257852557793, "five_p": { "contig_id": 4, "pos": 31438857 }, "three_p": { "contig_id": 4, "pos": 31438857 } } }, "unaligned_range": { "end": 78776840, "start": 68927386 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 9050655189390037140, "five_p": { "contig_id": 6, "pos": 59452521 }, "three_p": { "contig_id": 6, "pos": 59452876 } }, "start": { "bc_hash": 12612432056225637305, "five_p": { "contig_id": 5, "pos": 60854485 }, "three_p": { "contig_id": 5, "pos": 60854924 } } }, "unaligned_range": { "end": 88620441, "start": 78776840 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 5825932741504553481, "five_p": { "contig_id": 7, "pos": 30851613 }, "three_p": { "contig_id": 7, "pos": 30851844 } }, "start": { "bc_hash": 9050655189390037140, "five_p": { "contig_id": 6, "pos": 59452521 }, "three_p": { "contig_id": 6, "pos": 59452876 } } }, "unaligned_range": { "end": 98469523, "start": 88620441 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 9809247189969436483, "five_p": { "contig_id": 8, "pos": 22677209 }, "three_p": { "contig_id": 8, "pos": 22677308 } }, "start": { "bc_hash": 5825932741504553481, "five_p": { "contig_id": 7, "pos": 30851613 }, "three_p": { "contig_id": 7, "pos": 30851844 } } }, "unaligned_range": { "end": 108319378, "start": 98469523 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 6901458852720399445, "five_p": { "contig_id": 9, "pos": 5707913 }, "three_p": { "contig_id": 9, "pos": 5708015 } }, "start": { "bc_hash": 9809247189969436483, "five_p": { "contig_id": 8, "pos": 22677209 }, "three_p": { "contig_id": 8, "pos": 22677308 } } }, "unaligned_range": { "end": 118162736, "start": 108319378 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 7706420581295832769, "five_p": { "contig_id": 10, "pos": 14097073 }, "three_p": { "contig_id": 10, "pos": 14097400 } }, "start": { "bc_hash": 6901458852720399445, "five_p": { "contig_id": 9, "pos": 5707913 }, "three_p": { "contig_id": 9, "pos": 5708015 } } }, "unaligned_range": { "end": 128013981, "start": 118162736 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 4717419089542018323, "five_p": { "contig_id": 11, "pos": 19195257 }, "three_p": { "contig_id": 11, "pos": 19195468 } }, "start": { "bc_hash": 7706420581295832769, "five_p": { "contig_id": 10, "pos": 14097073 }, "three_p": { "contig_id": 10, "pos": 14097400 } } }, "unaligned_range": { "end": 137853766, "start": 128013981 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 7390290658344111926, "five_p": { "contig_id": 11, "pos": 162769283 }, "three_p": { "contig_id": 11, "pos": 162769444 } }, "start": { "bc_hash": 4717419089542018323, "five_p": { "contig_id": 11, "pos": 19195257 }, "three_p": { "contig_id": 11, "pos": 19195468 } } }, "unaligned_range": { "end": 147704243, "start": 137853766 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 1414738266847729441, "five_p": { "contig_id": 12, "pos": 24845224 }, "three_p": { "contig_id": 12, "pos": 24845370 } }, "start": { "bc_hash": 7390290658344111926, "five_p": { "contig_id": 11, "pos": 162769283 }, "three_p": { "contig_id": 11, "pos": 162769444 } } }, "unaligned_range": { "end": 157554740, "start": 147704243 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 8249580164917826841, "five_p": { "contig_id": 13, "pos": 33230003 }, "three_p": { "contig_id": 13, "pos": 33230165 } }, "start": { "bc_hash": 1414738266847729441, "five_p": { "contig_id": 12, "pos": 24845224 }, "three_p": { "contig_id": 12, "pos": 24845370 } } }, "unaligned_range": { "end": 167396790, "start": 157554740 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 11055018929839669582, "five_p": { "contig_id": 15, "pos": 17455569 }, "three_p": { "contig_id": 15, "pos": 17455811 } }, "start": { "bc_hash": 8249580164917826841, "five_p": { "contig_id": 13, "pos": 33230003 }, "three_p": { "contig_id": 13, "pos": 33230165 } } }, "unaligned_range": { "end": 177246313, "start": 167396790 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 10943464994866171837, "five_p": { "contig_id": 15, "pos": 125871561 }, "three_p": { "contig_id": 15, "pos": 125872030 } }, "start": { "bc_hash": 11055018929839669582, "five_p": { "contig_id": 15, "pos": 17455569 }, "three_p": { "contig_id": 15, "pos": 17455811 } } }, "unaligned_range": { "end": 187088399, "start": 177246313 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 1408230609752782274, "five_p": { "contig_id": 16, "pos": 27739777 }, "three_p": { "contig_id": 16, "pos": 27740168 } }, "start": { "bc_hash": 10943464994866171837, "five_p": { "contig_id": 15, "pos": 125871561 }, "three_p": { "contig_id": 15, "pos": 125872030 } } }, "unaligned_range": { "end": 196938315, "start": 187088399 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": null, "five_p": { "contig_id": 16, "pos": 155532486 }, "three_p": { "contig_id": 16, "pos": 155532585 } }, "start": { "bc_hash": 1408230609752782274, "five_p": { "contig_id": 16, "pos": 27739777 }, "three_p": { "contig_id": 16, "pos": 27740168 } } }, "unaligned_range": { "end": 206788324, "start": 196938315 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 2888063851721979643, "five_p": { "contig_id": 17, "pos": 82074597 }, "three_p": { "contig_id": 17, "pos": 82075040 } }, "start": { "bc_hash": null, "five_p": { "contig_id": 16, "pos": 155532486 }, "three_p": { "contig_id": 16, "pos": 155532585 } } }, "unaligned_range": { "end": 216630509, "start": 206788324 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 1746211458711737478, "five_p": { "contig_id": 18, "pos": 35948205 }, "three_p": { "contig_id": 18, "pos": 35948396 } }, "start": { "bc_hash": 2888063851721979643, "five_p": { "contig_id": 17, "pos": 82074597 }, "three_p": { "contig_id": 17, "pos": 82075040 } } }, "unaligned_range": { "end": 226481193, "start": 216630509 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 8680657159688990223, "five_p": { "contig_id": 18, "pos": 150202153 }, "three_p": { "contig_id": 18, "pos": 150202669 } }, "start": { "bc_hash": 1746211458711737478, "five_p": { "contig_id": 18, "pos": 35948205 }, "three_p": { "contig_id": 18, "pos": 35948396 } } }, "unaligned_range": { "end": 236324095, "start": 226481193 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 6652128048880124057, "five_p": { "contig_id": 19, "pos": 73831259 }, "three_p": { "contig_id": 19, "pos": 73831335 } }, "start": { "bc_hash": 8680657159688990223, "five_p": { "contig_id": 18, "pos": 150202153 }, "three_p": { "contig_id": 18, "pos": 150202669 } } }, "unaligned_range": { "end": 246173179, "start": 236324095 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 892903012720674943, "five_p": { "contig_id": 20, "pos": 9980356 }, "three_p": { "contig_id": 20, "pos": 9980560 } }, "start": { "bc_hash": 6652128048880124057, "five_p": { "contig_id": 19, "pos": 73831259 }, "three_p": { "contig_id": 19, "pos": 73831335 } } }, "unaligned_range": { "end": 256025112, "start": 246173179 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 8112155414684930721, "five_p": { "contig_id": 20, "pos": 124496707 }, "three_p": { "contig_id": 20, "pos": 124496791 } }, "start": { "bc_hash": 892903012720674943, "five_p": { "contig_id": 20, "pos": 9980356 }, "three_p": { "contig_id": 20, "pos": 9980560 } } }, "unaligned_range": { "end": 265864533, "start": 256025112 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 11616229956343488537, "five_p": { "contig_id": 21, "pos": 96331661 }, "three_p": { "contig_id": 21, "pos": 96331726 } }, "start": { "bc_hash": 8112155414684930721, "five_p": { "contig_id": 20, "pos": 124496707 }, "three_p": { "contig_id": 20, "pos": 124496791 } } }, "unaligned_range": { "end": 275715913, "start": 265864533 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": { "bc_hash": 5319151814872361320, "five_p": { "contig_id": 22, "pos": 16024 }, "three_p": { "contig_id": 22, "pos": 16079 } }, "start": { "bc_hash": 11616229956343488537, "five_p": { "contig_id": 21, "pos": 96331661 }, "three_p": { "contig_id": 21, "pos": 96331726 } } }, "unaligned_range": { "end": 285557057, "start": 275715913 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 4, "__threads": 2, "__vmem_gb": 7, "aligned_range": { "end": null, "start": { "bc_hash": 5319151814872361320, "five_p": { "contig_id": 22, "pos": 16024 }, "three_p": { "contig_id": 22, "pos": 16079 } } }, "unaligned_range": { "end": null, "start": 285557057 } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "aligned_shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-u9761b6a514/files/aligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-u9761b6a514/files/aligned_chunk.shard" ], "waiting": false }, { "id": "unaligned_shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk00-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk01-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk02-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk03-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk04-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk05-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk06-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk07-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk08-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk09-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk10-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk11-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk12-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk13-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk14-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk15-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk16-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk17-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk18-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk19-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk20-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk21-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk22-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk23-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk24-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk25-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk26-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk27-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk28-u9761b6a514/files/unaligned_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/ALIGN_ATAC_READS/fork0/chnk29-u9761b6a514/files/unaligned_chunk.shard" ], "waiting": false }, { "id": "num_read_pairs", "type": "int", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": 295403617, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_counts", "type": "bch.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u9761b69f69/files/barcode_counts.bch.bincode", "waiting": false }, { "id": "assay", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "arc", "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false } ], "Return": [ { "id": "deduped_shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk00-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk01-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk02-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk03-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk04-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk05-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk06-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk07-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk08-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk09-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk10-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk11-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk12-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk13-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk14-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk15-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk16-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk17-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk18-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk19-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk20-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk21-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk22-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk23-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk24-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk25-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk26-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk27-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk28-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk29-u9761b6cc24/files/deduped_chunk.shard" ], "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/singlecell.csv", "waiting": false }, { "id": "insert_sizes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/insert_sizes.csv", "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/summary.json", "waiting": false }, { "id": "frag_bc_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/frag_bc_counts.json", "waiting": false }, { "id": "max_items_per_footprint", "type": "int", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": 6538, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.ALIGN_ATAC_READS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian mark_atac_duplicates" }, { "name": "WRITE_ATAC_BAM", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 0, "range": { "end": { "pos": { "contig_id": 0, "pos": 180100720 } }, "start": null } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 1, "range": { "end": { "pos": { "contig_id": 1, "pos": 128125722 } }, "start": { "pos": { "contig_id": 0, "pos": 180100720 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 2, "range": { "end": { "pos": { "contig_id": 3, "pos": 49322883 } }, "start": { "pos": { "contig_id": 1, "pos": 128125722 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 3, "range": { "end": { "pos": { "contig_id": 5, "pos": 63923318 } }, "start": { "pos": { "contig_id": 3, "pos": 49322883 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 4, "range": { "end": { "pos": { "contig_id": 7, "pos": 52192298 } }, "start": { "pos": { "contig_id": 5, "pos": 63923318 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 5, "range": { "end": { "pos": { "contig_id": 9, "pos": 35527615 } }, "start": { "pos": { "contig_id": 7, "pos": 52192298 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 6, "range": { "end": { "pos": { "contig_id": 11, "pos": 49085755 } }, "start": { "pos": { "contig_id": 9, "pos": 35527615 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 7, "range": { "end": { "pos": { "contig_id": 12, "pos": 32124902 } }, "start": { "pos": { "contig_id": 11, "pos": 49085755 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 8, "range": { "end": { "pos": { "contig_id": 15, "pos": 39934815 } }, "start": { "pos": { "contig_id": 12, "pos": 32124902 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 9, "range": { "end": { "pos": { "contig_id": 16, "pos": 62607734 } }, "start": { "pos": { "contig_id": 15, "pos": 39934815 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 10, "range": { "end": { "pos": { "contig_id": 17, "pos": 134257931 } }, "start": { "pos": { "contig_id": 16, "pos": 62607734 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 11, "range": { "end": { "pos": { "contig_id": 18, "pos": 160167818 } }, "start": { "pos": { "contig_id": 17, "pos": 134257931 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 12, "range": { "end": { "pos": { "contig_id": 20, "pos": 30395723 } }, "start": { "pos": { "contig_id": 18, "pos": 160167818 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 13, "range": { "end": { "pos": { "contig_id": 21, "pos": 127805785 } }, "start": { "pos": { "contig_id": 20, "pos": 30395723 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_id": 14, "range": { "end": null, "start": { "pos": { "contig_id": 21, "pos": 127805785 } } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "num_read_pairs", "type": "int", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "matchedFork": null, "value": 295403617, "waiting": false }, { "id": "deduped_shards", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk00-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk01-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk02-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk03-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk04-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk05-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk06-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk07-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk08-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk09-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk10-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk11-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk12-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk13-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk14-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk15-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk16-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk17-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk18-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk19-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk20-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk21-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk22-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk23-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk24-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk25-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk26-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk27-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk28-u9761b6cc24/files/deduped_chunk.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk29-u9761b6cc24/files/deduped_chunk.shard" ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "fastq_defs", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": [ { "read1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R1_001.fastq.gz", "read2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R3_001.fastq.gz", "reads_interleaved": false, "barcode": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R2_001.fastq.gz", "sample_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_I1_001.fastq.gz", "gem_group": 1, "subsample_rate": 1.0, "read_group": "samp24_CR_out:MissingLibrary:1:H5CK3DSX2:2", "chemistry": null, "fastq_mode": "ILMN_BCL2FASTQ" } ], "waiting": false }, { "id": "max_items_per_footprint", "type": "int", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": 6538, "waiting": false } ], "Return": [ { "id": "possorted_bam", "type": "bam", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam", "waiting": false }, { "id": "possorted_bam_index", "type": "bam.bai", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/WRITE_ATAC_BAM/fork0/join-u9761b6d0e6/files/possorted_bam.bam.bai", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MAKE_ATAC_SHARDS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.WRITE_ATAC_BAM" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian write_atac_bam" }, { "name": "_PEAK_CALLER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "assay", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "arc", "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "custom_peaks", "type": "bed", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "disable_bigwig", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false } ], "Return": [ { "id": "cut_sites", "type": "bigwig", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-u9761b6d137/files/cut_sites.bigwig", "waiting": false }, { "id": "count_dict", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/count_dict.json", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "peak_metrics", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peak_metrics.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "CONVERT_SIGNAL_TRACK", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "cut_sites", "type": "bedgraph", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/cut_sites.bedgraph", "waiting": false } ], "Return": [ { "id": "cut_sites", "type": "bigwig", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/CONVERT_SIGNAL_TRACK/fork0/chnk0-u9761b6d137/files/cut_sites.bigwig", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.CONVERT_SIGNAL_TRACK" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/convert_signal_track" }, { "name": "COUNT_CUT_SITES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 4, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 8, "__threads": 4, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false } ], "Return": [ { "id": "cut_sites", "type": "bedgraph", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/cut_sites.bedgraph", "waiting": false }, { "id": "count_dict", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/count_dict.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian count_cut_sites" }, { "name": "DETECT_PEAKS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 5, "__vmem_gb": 8 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr2" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr3" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr4" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr5" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr6" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr7" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chrX" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr8" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr9" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr11" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr10" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr12" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr13" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr14" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr15" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr16" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr17" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr18" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr20" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr19" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chrY", "KI270713.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr22", "KI270711.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "chr21", "KI270726.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "KI270728.1", "KI270721.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "KI270727.1", "KI270731.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "GL000009.2", "GL000218.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "GL000194.1", "GL000213.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "GL000205.2", "KI270734.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11, "contigs": [ "GL000195.1", "GL000219.1" ], "threshold": 64 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "assay", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "arc", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "cut_sites", "type": "bedgraph", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/cut_sites.bedgraph", "waiting": false }, { "id": "count_dict", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/count_dict.json", "waiting": false }, { "id": "custom_peaks", "type": "bed", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false } ], "Return": [ { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "peak_metrics", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peak_metrics.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/detect_peaks" }, { "name": "_FASTQ_STAGER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "atac_sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "atac_barcode_whitelist", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "atac_subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "rna_chemistry", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "ARC-v1", "waiting": false }, { "id": "rna_custom_chemistry_def", "type": "ChemistryDef", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "atac_chunks", "type": "FastqDef[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": [ { "read1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R1_001.fastq.gz", "read2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R3_001.fastq.gz", "reads_interleaved": false, "barcode": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R2_001.fastq.gz", "sample_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_I1_001.fastq.gz", "gem_group": 1, "subsample_rate": 1.0, "read_group": "samp24_CR_out:MissingLibrary:1:H5CK3DSX2:2", "chemistry": null, "fastq_mode": "ILMN_BCL2FASTQ" } ], "waiting": false }, { "id": "rna_chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "rna_chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "atac_barcode_whitelist_path", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ATAC_SETUP_CHUNKS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/ATAC_SETUP_CHUNKS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "737K-arc-v1", "waiting": false } ], "Return": [ { "id": "chunks", "type": "FastqDef[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": [ { "read1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R1_001.fastq.gz", "read2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R3_001.fastq.gz", "reads_interleaved": false, "barcode": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_R2_001.fastq.gz", "sample_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq/samp24_S1_L002_I1_001.fastq.gz", "gem_group": 1, "subsample_rate": 1.0, "read_group": "samp24_CR_out:MissingLibrary:1:H5CK3DSX2:2", "chemistry": null, "fastq_mode": "ILMN_BCL2FASTQ" } ], "waiting": false }, { "id": "barcode_whitelist_path", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS", "matchedFork": null, "value": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.ATAC_SETUP_CHUNKS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/setup_chunks" }, { "name": "GEX_SETUP_CHUNKS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_FASTQ_STAGER/GEX_SETUP_CHUNKS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Gene Expression", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "chemistry_name", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "ARC-v1", "waiting": false }, { "id": "custom_chemistry_def", "type": "ChemistryDef", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "default_library_type", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": "737K-arc-v1", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian setup_chunks" }, { "name": "_GEX_CELLS_REPORTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "recovered_cells", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1000, "waiting": false }, { "id": "force_cells", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "slfe_feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "target_panel_summary", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_set_name", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "matrices_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "read_chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "report_mol_inputs", "type": "bui[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_umi_info.bui" ], "waiting": false }, { "id": "matrix_computer_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u9761b6d516/files/summary.json", "waiting": false }, { "id": "barcode_summary", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u9761b6d4fd/files/barcode_summary.h5", "waiting": false }, { "id": "filtered_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "filter_barcodes_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u9761b6d563/files/summary.json", "waiting": false }, { "id": "per_barcode_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/per_barcode_metrics.csv", "waiting": false }, { "id": "include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "multi_config_sha", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "barcode_index", "type": "bi.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9761b6bfc4/files/barcode_index.bi.bincode", "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u9761b6d7a5/files/summary.json", "waiting": false }, { "id": "molecule_info", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u9761b6d563/files/molecule_info_non_multiplexed.h5", "waiting": false }, { "id": "merged_subsampling_metrics", "type": "pickle", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u9761b6d59c/files/merged_metrics.pickle", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "SUBSAMPLE_READS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 6, "__vmem_gb": 9 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "chunk_len": 10000631, "chunk_start": 0, "subsample_info": [ { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 5000, "library_subsample_rates": [ 0.021542738898556003 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 0.043085477797112005 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 20000, "library_subsample_rates": [ 0.08617095559422401 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 23209, "library_subsample_rates": [ 0.09999708541931725 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 30000, "library_subsample_rates": [ 0.129256433391336 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 46419, "library_subsample_rates": [ 0.19999847938641419 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.21542738898556 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 69629, "library_subsample_rates": [ 0.29999987335351114 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 92838, "library_subsample_rates": [ 0.39999695877282837 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 116048, "library_subsample_rates": [ 0.4999983527399253 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 139258, "library_subsample_rates": [ 0.5999997467070223 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 162467, "library_subsample_rates": [ 0.6999968321263396 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 185677, "library_subsample_rates": [ 0.7999982260934365 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 208887, "library_subsample_rates": [ 0.8999996200605335 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 232096, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 5000, "library_subsample_rates": [ 0.04778475476322896 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 0.09556950952645792 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 10463, "library_subsample_rates": [ 0.09999437781753293 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 20000, "library_subsample_rates": [ 0.19113901905291583 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 20927, "library_subsample_rates": [ 0.1999983125860185 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 30000, "library_subsample_rates": [ 0.28670852857937373 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 31390, "library_subsample_rates": [ 0.2999926904035514 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 41854, "library_subsample_rates": [ 0.399996625172037 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.4778475476322896 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 52317, "library_subsample_rates": [ 0.4999910029895699 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 62781, "library_subsample_rates": [ 0.5999949377580555 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 73245, "library_subsample_rates": [ 0.699998872526541 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 83708, "library_subsample_rates": [ 0.799993250344074 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 94172, "library_subsample_rates": [ 0.8999971851125596 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 104635, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 4.278597596535452e-05 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.0002139298798267726 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 100000, "library_subsample_rates": [ 0.0004278597596535452 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 250000, "library_subsample_rates": [ 0.0010696493991338629 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 500000, "library_subsample_rates": [ 0.0021392987982677258 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 1000000, "library_subsample_rates": [ 0.0042785975965354515 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 2500000, "library_subsample_rates": [ 0.010696493991338629 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 5000000, "library_subsample_rates": [ 0.021392987982677258 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 7500000, "library_subsample_rates": [ 0.03208948197401589 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 10000000, "library_subsample_rates": [ 0.042785975965354515 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 23372144, "library_subsample_rates": [ 0.09999999914428048 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 46744288, "library_subsample_rates": [ 0.19999999828856097 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 50000000, "library_subsample_rates": [ 0.21392987982677258 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 70116432, "library_subsample_rates": [ 0.29999999743284145 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 93488576, "library_subsample_rates": [ 0.39999999657712193 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 100000000, "library_subsample_rates": [ 0.42785975965354517 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 116860721, "library_subsample_rates": [ 0.5 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 140232865, "library_subsample_rates": [ 0.5999999991442805 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 163605009, "library_subsample_rates": [ 0.699999998288561 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 186977153, "library_subsample_rates": [ 0.7999999974328414 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 210349297, "library_subsample_rates": [ 0.8999999965771219 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 233721442, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 1000000000, "library_subsample_rates": [ 0.0 ] } ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "chunk_len": 5231880, "chunk_start": 10000631, "subsample_info": [ { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 5000, "library_subsample_rates": [ 0.021542738898556003 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 0.043085477797112005 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 20000, "library_subsample_rates": [ 0.08617095559422401 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 23209, "library_subsample_rates": [ 0.09999708541931725 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 30000, "library_subsample_rates": [ 0.129256433391336 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 46419, "library_subsample_rates": [ 0.19999847938641419 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.21542738898556 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 69629, "library_subsample_rates": [ 0.29999987335351114 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 92838, "library_subsample_rates": [ 0.39999695877282837 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 116048, "library_subsample_rates": [ 0.4999983527399253 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 139258, "library_subsample_rates": [ 0.5999997467070223 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 162467, "library_subsample_rates": [ 0.6999968321263396 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 185677, "library_subsample_rates": [ 0.7999982260934365 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 208887, "library_subsample_rates": [ 0.8999996200605335 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_rpc", "target_read_pairs_per_cell": 232096, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 5000, "library_subsample_rates": [ 0.04778475476322896 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 0.09556950952645792 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 10463, "library_subsample_rates": [ 0.09999437781753293 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 20000, "library_subsample_rates": [ 0.19113901905291583 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 20927, "library_subsample_rates": [ 0.1999983125860185 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 30000, "library_subsample_rates": [ 0.28670852857937373 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 31390, "library_subsample_rates": [ 0.2999926904035514 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 41854, "library_subsample_rates": [ 0.399996625172037 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.4778475476322896 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 52317, "library_subsample_rates": [ 0.4999910029895699 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 62781, "library_subsample_rates": [ 0.5999949377580555 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 73245, "library_subsample_rates": [ 0.699998872526541 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 83708, "library_subsample_rates": [ 0.799993250344074 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 94172, "library_subsample_rates": [ 0.8999971851125596 ] }, { "library_type": "Gene Expression", "subsample_type": "conf_mapped_barcoded_filtered_bc_rpc", "target_read_pairs_per_cell": 104635, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 10000, "library_subsample_rates": [ 4.278597596535452e-05 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 50000, "library_subsample_rates": [ 0.0002139298798267726 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 100000, "library_subsample_rates": [ 0.0004278597596535452 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 250000, "library_subsample_rates": [ 0.0010696493991338629 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 500000, "library_subsample_rates": [ 0.0021392987982677258 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 1000000, "library_subsample_rates": [ 0.0042785975965354515 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 2500000, "library_subsample_rates": [ 0.010696493991338629 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 5000000, "library_subsample_rates": [ 0.021392987982677258 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 7500000, "library_subsample_rates": [ 0.03208948197401589 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 10000000, "library_subsample_rates": [ 0.042785975965354515 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 23372144, "library_subsample_rates": [ 0.09999999914428048 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 46744288, "library_subsample_rates": [ 0.19999999828856097 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 50000000, "library_subsample_rates": [ 0.21392987982677258 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 70116432, "library_subsample_rates": [ 0.29999999743284145 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 93488576, "library_subsample_rates": [ 0.39999999657712193 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 100000000, "library_subsample_rates": [ 0.42785975965354517 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 116860721, "library_subsample_rates": [ 0.5 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 140232865, "library_subsample_rates": [ 0.5999999991442805 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 163605009, "library_subsample_rates": [ 0.699999998288561 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 186977153, "library_subsample_rates": [ 0.7999999974328414 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 210349297, "library_subsample_rates": [ 0.8999999965771219 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 233721442, "library_subsample_rates": [ 1.0 ] }, { "library_type": "Gene Expression", "subsample_type": "raw_reads", "target_read_pairs_per_cell": 1000000000, "library_subsample_rates": [ 0.0 ] } ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "molecule_info", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u9761b6d563/files/molecule_info_non_multiplexed.h5", "waiting": false }, { "id": "filtered_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "target_mode", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u9761b6d59c/files/summary.json", "waiting": false }, { "id": "merged_metrics", "type": "pickle", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u9761b6d59c/files/merged_metrics.pickle", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/counter/subsample_reads" }, { "name": "SUMMARIZE_BASIC_REPORTS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3, "__vmem_gb": 6 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "matrices_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "filtered_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "per_barcode_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/per_barcode_metrics.csv", "waiting": false }, { "id": "matrix_computer_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u9761b6d516/files/summary.json", "waiting": false }, { "id": "barcode_summary", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u9761b6d4fd/files/barcode_summary.h5", "waiting": false }, { "id": "recovered_cells", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1000, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "cell_bcs_only", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "summary_jsons", "type": "json[]", "mode": "", "node": null, "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u9761b6d516/files/summary.json", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u9761b6d59c/files/summary.json", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u9761b6d563/files/non_multiplexed_summary.json", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u9761b6d563/files/summary.json" ], "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u9761b6d7a5/files/summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUBSAMPLE_READS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.SUMMARIZE_BASIC_REPORTS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/counter/summarize_basic_reports" }, { "name": "WRITE_MOLECULE_INFO", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 16, "__vmem_gb": 19 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 16, "__threads": 1, "__vmem_gb": 19 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "counts_bc_order", "type": "bui[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_umi_info.bui" ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "read_chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "target_panel_summary", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_set_name", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "matrix_computer_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u9761b6d516/files/summary.json", "waiting": false }, { "id": "recovered_cells", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1000, "waiting": false }, { "id": "force_cells", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "filtered_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "multi_config_sha", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "sample_barcodes_json", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "per_sample_metrics", "type": "SampleMetrics[]", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "barcode_index", "type": "bi.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9761b6bfc4/files/barcode_index.bi.bincode", "waiting": false } ], "Return": [ { "id": "single_mol_info", "type": "SampleMoleculeInfo", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": { "h5_file": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u9761b6d563/files/molecule_info_non_multiplexed.h5", "sample": "non_multiplexed", "summary": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u9761b6d563/files/non_multiplexed_summary.json" }, "waiting": false }, { "id": "multi_mol_info", "type": "SampleMoleculeInfo[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO", "matchedFork": null, "value": null, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_CELLS_REPORTER.WRITE_MOLECULE_INFO" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_molecule_info" }, { "name": "_GEX_MATRIX_COMPUTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "barcodes_under_tissue", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "is_pd", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "libraries_to_translate", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [], "waiting": false }, { "id": "chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "initial_reads", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "r1_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "r2_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "trim_polya_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "trim_tso_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "feature_reference", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_features", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_set", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_set_name", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "aligner", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "disable_target_umi_filter", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "rps_limit", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "write_bc_counts_json", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false } ], "Return": [ { "id": "slfe_feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "barcode_correction_csv", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u9761b6bfc5/files/barcode_summary.csv", "waiting": false }, { "id": "barcode_summary", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u9761b6d4fd/files/barcode_summary.h5", "waiting": false }, { "id": "raw_gene_bc_matrices_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "raw_gene_bc_matrices_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix", "waiting": false }, { "id": "read_shards", "type": "ReadShards", "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/valid_shard.shard" ], "invalid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/invalid_shard.shard" ], "valid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/valid.shard" ] }, "waiting": false }, { "id": "report_mol_inputs", "type": "bui[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_umi_info.bui" ], "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u9761b6d516/files/summary.json", "waiting": false }, { "id": "annotation_files", "type": "ann.bincode.lz4[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4" ], "waiting": false }, { "id": "per_barcode_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/per_barcode_metrics.csv", "waiting": false }, { "id": "per_barcode_metrics_shard", "type": "bmsf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/metrics_shard.bmsf" ], "waiting": false }, { "id": "bc_umi_info", "type": "bui[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_umi_info.bui" ], "waiting": false }, { "id": "bam_header", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u9761b6bfc5/files/bam_header", "waiting": false }, { "id": "alignments", "type": "asf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/pos_sorted.asf" ], "waiting": false }, { "id": "multi_metrics", "type": "SampleMetrics[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": null, "waiting": false }, { "id": "gem_well_alignment_metrics", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/summary.json", "waiting": false }, { "id": "barcode_index", "type": "bi.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9761b6bfc4/files/barcode_index.bi.bincode", "waiting": false }, { "id": "sequencing_metrics", "type": "smf.json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/sequencing_metrics.smf.json", "waiting": false }, { "id": "bc_counts_json", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/bc_counts_json.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ALIGN_AND_COUNT", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 16, "__vmem_gb": 19 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 16, "__threads": 4, "__vmem_gb": 19, "range": { "end": { "gem_group": 1, "sequence": "CAAACATGTCACTTAA", "valid": false }, "start": null }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 16, "__threads": 4, "__vmem_gb": 19, "range": { "end": { "gem_group": 1, "sequence": "CTCAGTCATCATCAGG", "valid": false }, "start": { "gem_group": 1, "sequence": "CAAACATGTCACTTAA", "valid": false } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 16, "__threads": 4, "__vmem_gb": 19, "range": { "end": { "gem_group": 1, "sequence": "GCTCTGCACTTCCTGC", "valid": false }, "start": { "gem_group": 1, "sequence": "CTCAGTCATCATCAGG", "valid": false } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 16, "__threads": 4, "__vmem_gb": 19, "range": { "end": { "gem_group": 1, "sequence": "TCATTGCTGGTGCTCT", "valid": false }, "start": { "gem_group": 1, "sequence": "GCTCTGCACTTCCTGC", "valid": false } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 16, "__threads": 4, "__vmem_gb": 19, "range": { "end": { "gem_group": 1, "sequence": "AAACAGCCAAATTGCT", "valid": true }, "start": { "gem_group": 1, "sequence": "TCATTGCTGGTGCTCT", "valid": false } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "ACTTTGTTCACGCCAA", "valid": true }, "start": { "gem_group": 1, "sequence": "AAACAGCCAAATTGCT", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "AGGCTAAAGGTTTACA", "valid": true }, "start": { "gem_group": 1, "sequence": "ACTTTGTTCACGCCAA", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "CATAATCCAACACCTA", "valid": true }, "start": { "gem_group": 1, "sequence": "AGGCTAAAGGTTTACA", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "CGTGTTACACTGACCG", "valid": true }, "start": { "gem_group": 1, "sequence": "CATAATCCAACACCTA", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "GAACCAGCATTTAAGC", "valid": true }, "start": { "gem_group": 1, "sequence": "CGTGTTACACTGACCG", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "GCGATATTCTTGCAAA", "valid": true }, "start": { "gem_group": 1, "sequence": "GAACCAGCATTTAAGC", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "GTAAGGTCATGTTGGC", "valid": true }, "start": { "gem_group": 1, "sequence": "GCGATATTCTTGCAAA", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "TAGTTGTCATGATTGT", "valid": true }, "start": { "gem_group": 1, "sequence": "GTAAGGTCATGTTGGC", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": { "gem_group": 1, "sequence": "TGCTTCCAGTTAGCCG", "valid": true }, "start": { "gem_group": 1, "sequence": "TAGTTGTCATGATTGT", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 21, "__threads": 4, "__vmem_gb": 24, "range": { "end": null, "start": { "gem_group": 1, "sequence": "TGCTTCCAGTTAGCCG", "valid": true } }, "read_ann_subsample_rate": 0.21392987668514252 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "read_chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "read_shards", "type": "ReadShards", "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/valid_shard.shard" ], "invalid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/invalid_shard.shard" ], "valid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/valid.shard" ] }, "waiting": false }, { "id": "feature_counts", "type": "fbc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/feature_counts.fbc.bincode", "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "target_set", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "aligner", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "aligner_subsample_rate", "type": "float", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE", "matchedFork": null, "value": null, "waiting": false }, { "id": "is_pd", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "transcriptome_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 30, "waiting": false }, { "id": "trim_polya_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "trim_tso_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "targeted_umi_min_read_count", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "total_barcode_counts", "type": "tbcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/total_barcode_counts.tbcc.bincode", "waiting": false }, { "id": "barcode_subset", "type": "blf.json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "counts_bc_order", "type": "csf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_sort.csf" ], "waiting": false }, { "id": "counts_feature_order", "type": "csf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/feature_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/feature_sort.csf" ], "waiting": false }, { "id": "bc_umi_info", "type": "bui[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_umi_info.bui" ], "waiting": false }, { "id": "pos_sorted", "type": "asf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/pos_sorted.asf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/pos_sorted.asf" ], "waiting": false }, { "id": "bam_header", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u9761b6bfc5/files/bam_header", "waiting": false }, { "id": "barcode_summary", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u9761b6bfc5/files/barcode_summary.csv", "waiting": false }, { "id": "annotation_files", "type": "ann.bincode.lz4[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_0.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_1.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_2.ann.bincode.lz4", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/read_annotations_3.ann.bincode.lz4" ], "waiting": false }, { "id": "per_barcode_metrics", "type": "bmsf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/metrics_shard.bmsf" ], "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian align_and_count" }, { "name": "BARCODE_CORRECTION", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 4, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "AATAGCTGAAGTTATG", "valid": false }, "start": null } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "ACCATTAAGTGCTGGG", "valid": false }, "start": { "gem_group": 1, "sequence": "AATAGCTGAAGTTATG", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "ACTCACTGGCCCAGAA", "valid": false }, "start": { "gem_group": 1, "sequence": "ACCATTAAGTGCTGGG", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "AGGAGTGAGGCCTGGT", "valid": false }, "start": { "gem_group": 1, "sequence": "ACTCACTGGCCCAGAA", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "ATCATCAAGCCTTGGC", "valid": false }, "start": { "gem_group": 1, "sequence": "AGGAGTGAGGCCTGGT", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "ATTTACTGGTGAGCAG", "valid": false }, "start": { "gem_group": 1, "sequence": "ATCATCAAGCCTTGGC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "CACGACCATAATCCGA", "valid": false }, "start": { "gem_group": 1, "sequence": "ATTTACTGGTGAGCAG", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "CATTCAAGTTTTGAGC", "valid": false }, "start": { "gem_group": 1, "sequence": "CACGACCATAATCCGA", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "CCGTGCTGAGGCAGGA", "valid": false }, "start": { "gem_group": 1, "sequence": "CATTCAAGTTTTGAGC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "CGATTGACCATCCTGG", "valid": false }, "start": { "gem_group": 1, "sequence": "CCGTGCTGAGGCAGGA", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "CGTTGCAAGCAGCTTA", "valid": false }, "start": { "gem_group": 1, "sequence": "CGATTGACCATCCTGG", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "CTCCCAACAGAGATCT", "valid": false }, "start": { "gem_group": 1, "sequence": "CGTTGCAAGCAGCTTA", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "CTGGCCAAGTCTTTTT", "valid": false }, "start": { "gem_group": 1, "sequence": "CTCCCAACAGAGATCT", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GAAAATCTGCCCCTCC", "valid": false }, "start": { "gem_group": 1, "sequence": "CTGGCCAAGTCTTTTT", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GATCGATTAGCACCTC", "valid": false }, "start": { "gem_group": 1, "sequence": "GAAAATCTGCCCCTCC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GCCACTACAAAGGCAA", "valid": false }, "start": { "gem_group": 1, "sequence": "GATCGATTAGCACCTC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GCTAAGCGTGCATTGC", "valid": false }, "start": { "gem_group": 1, "sequence": "GCCACTACAAAGGCAA", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GGAAATCCTGGCTGTC", "valid": false }, "start": { "gem_group": 1, "sequence": "GCTAAGCGTGCATTGC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GGGTGTTGAGCTCCAC", "valid": false }, "start": { "gem_group": 1, "sequence": "GGAAATCCTGGCTGTC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GTACTGGAAGTTCTTT", "valid": false }, "start": { "gem_group": 1, "sequence": "GGGTGTTGAGCTCCAC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "GTGCTGGGTTTAACGC", "valid": false }, "start": { "gem_group": 1, "sequence": "GTACTGGAAGTTCTTT", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "TAACCAAGGCCTTAGT", "valid": false }, "start": { "gem_group": 1, "sequence": "GTGCTGGGTTTAACGC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "TATATGCTCAAGTGTC", "valid": false }, "start": { "gem_group": 1, "sequence": "TAACCAAGGCCTTAGT", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "TCCGCCAAGAACCAAG", "valid": false }, "start": { "gem_group": 1, "sequence": "TATATGCTCAAGTGTC", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "TCTACTAGTGAATGCA", "valid": false }, "start": { "gem_group": 1, "sequence": "TCCGCCAAGAACCAAG", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "TGCTCGCCAGGCTAAG", "valid": false }, "start": { "gem_group": 1, "sequence": "TCTACTAGTGAATGCA", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "TGTTGAAAAACTTTTA", "valid": false }, "start": { "gem_group": 1, "sequence": "TGCTCGCCAGGCTAAG", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": { "gem_group": 1, "sequence": "TTGAGACACCAGGTTT", "valid": false }, "start": { "gem_group": 1, "sequence": "TGTTGAAAAACTTTTA", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 4, "__threads": 4, "__vmem_gb": 7, "range": { "end": null, "start": { "gem_group": 1, "sequence": "TTGAGACACCAGGTTT", "valid": false } } }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "barcode_counts", "type": "bcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/barcode_counts.bcc.bincode", "waiting": false }, { "id": "barcode_segment_counts", "type": "bsc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/barcode_segment_counts.bsc.bincode", "waiting": false }, { "id": "chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "invalid_uncorrected", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/invalid.shard" ], "waiting": false }, { "id": "valid_read_metrics", "type": "bcm.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/bc_correct_summary.bcm.bincode", "waiting": false }, { "id": "libraries_to_translate", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [], "waiting": false } ], "Return": [ { "id": "valid_corrected", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/valid_shard.shard" ], "waiting": false }, { "id": "invalid", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/invalid_shard.shard" ], "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/summary.json", "waiting": false }, { "id": "corrected_barcode_counts", "type": "bcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/correct_barcode_counts.bcc.bincode", "waiting": false }, { "id": "total_barcode_counts", "type": "tbcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/total_barcode_counts.tbcc.bincode", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian barcode_correction" }, { "name": "COLLATE_METRICS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 4, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 4, "__vmem_gb": 4, "sample": "non_multiplexed" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "per_barcode_metrics", "type": "bmsf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/metrics_shard.bmsf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/metrics_shard.bmsf" ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "sample_barcodes_json", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/summary.json", "waiting": false }, { "id": "per_barcode_metrics", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/per_barcode_metrics.csv", "waiting": false }, { "id": "per_lib_type_metrics", "type": "map", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": {}, "waiting": false }, { "id": "multi_metrics", "type": "SampleMetrics[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "matchedFork": null, "value": null, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian collate_metrics" }, { "name": "MAKE_READ_SHARDS_STRUCT", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_READ_SHARDS_STRUCT/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "valid_reads", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/valid.shard" ], "waiting": false }, { "id": "corrected_reads", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/valid_shard.shard" ], "waiting": false }, { "id": "invalid_reads", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/invalid_shard.shard" ], "waiting": false } ], "Return": [ { "id": "read_shards", "type": "ReadShards", "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/valid_shard.shard" ], "invalid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/invalid_shard.shard" ], "valid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/valid.shard" ] }, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "MAKE_SHARD", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 4, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 6, "__threads": 2, "__vmem_gb": 9, "chunk_id": 0, "feature_reference": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "read_chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "r1_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "r2_length", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "subsample_rate", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "initial_read_pairs", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "target_features", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_set", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "target_set_name", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "feature_reference_path", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "libraries_to_translate", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [], "waiting": false }, { "id": "write_bc_counts_json", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false } ], "Return": [ { "id": "valid", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/valid.shard" ], "waiting": false }, { "id": "invalid", "type": "shard[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/invalid.shard" ], "waiting": false }, { "id": "barcode_counts", "type": "bcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/barcode_counts.bcc.bincode", "waiting": false }, { "id": "barcode_segment_counts", "type": "bsc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/barcode_segment_counts.bsc.bincode", "waiting": false }, { "id": "feature_counts", "type": "fbc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/feature_counts.fbc.bincode", "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/summary.json", "waiting": false }, { "id": "total_read_pairs", "type": "int", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": 233721442, "waiting": false }, { "id": "paired_end", "type": "bool", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": false, "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "bc_correct_summary", "type": "bcm.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/bc_correct_summary.bcm.bincode", "waiting": false }, { "id": "sequencing_metrics", "type": "smf.json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/sequencing_metrics.smf.json", "waiting": false }, { "id": "bc_counts_json", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/bc_counts_json.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian make_shard" }, { "name": "MERGE_METRICS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "summaries", "type": "json[]", "mode": "", "node": null, "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/summary.json", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/summary.json", null, "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u9761b6d4fd/files/summary.json" ], "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u9761b6d516/files/summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.COLLATE_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MERGE_METRICS" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian merge_metrics" }, { "name": "SET_ALIGNER_SUBSAMPLE_RATE", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/SET_ALIGNER_SUBSAMPLE_RATE/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "rps_limit", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "barcodes_under_tissue", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "corrected_barcode_counts", "type": "bcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/correct_barcode_counts.bcc.bincode", "waiting": false } ], "Return": [ { "id": "aligner_subsample_rate", "type": "float", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE", "matchedFork": null, "value": null, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.SET_ALIGNER_SUBSAMPLE_RATE" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian set_aligner_subsample_rate" }, { "name": "WRITE_BARCODE_INDEX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "barcode_counts", "type": "bcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/correct_barcode_counts.bcc.bincode", "waiting": false }, { "id": "barcodes_under_tissue", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "barcode_index", "type": "bi.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9761b6bfc4/files/barcode_index.bi.bincode", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_barcode_index" }, { "name": "WRITE_BARCODE_SUMMARY", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "unique_gem_groups", "type": "int[]", "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "waiting": false }, { "id": "bc_umi_info", "type": "bui[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_umi_info.bui", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_umi_info.bui" ], "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "barcode_index", "type": "bi.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9761b6bfc4/files/barcode_index.bi.bincode", "waiting": false } ], "Return": [ { "id": "barcode_summary", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u9761b6d4fd/files/barcode_summary.h5", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_SUMMARY" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_barcode_summary" }, { "name": "WRITE_H5_MATRIX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "counts", "type": "csf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_sort.csf" ], "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "barcode_index", "type": "bi.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9761b6bfc4/files/barcode_index.bi.bincode", "waiting": false } ], "Return": [ { "id": "matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_h5_matrix" }, { "name": "WRITE_MATRIX_MARKET", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "counts", "type": "csf[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9761b6bfc5/files/bc_sort.csf", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u9761b6bfc5/files/bc_sort.csf" ], "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "barcode_index", "type": "bi.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9761b6bfc4/files/barcode_index.bi.bincode", "waiting": false } ], "Return": [ { "id": "feature_bc_matrix", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_MATRIX_MARKET/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.ALIGN_AND_COUNT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_BARCODE_INDEX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_MATRIX_MARKET" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_lib martian write_matrix_market" }, { "name": "_SLFE_PARTIAL_FIRST_PASS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS", "state": "disabled", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/_SLFE_PARTIAL_FIRST_PASS/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "gem_well", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 1, "waiting": false }, { "id": "read_chunks", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": [ { "chemistry": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "chunk_id": 0, "fastq_id": null, "fastqs": { "i1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I1_001.fastq.gz", "i2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_I2_001.fastq.gz", "r1": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R1_001.fastq.gz", "r1_interleaved": false, "r2": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scRNA/fastq/samp24_S3_L001_R2_001.fastq.gz" }, "gem_group": 1, "library_id": 0, "library_type": "Gene Expression", "read_group": "samp24_CR_out:0:1:H5CWMDSX2:1", "read_lengths": {}, "subsample_rate": null } ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "read_shards", "type": "ReadShards", "mode": "", "node": null, "matchedFork": null, "value": { "corrected_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/valid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/valid_shard.shard" ], "invalid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk00-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk01-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk02-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk03-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk04-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk05-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk06-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk07-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk08-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk09-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk10-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk11-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk12-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk13-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk14-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk15-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk16-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk17-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk18-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk19-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk20-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk21-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk22-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk23-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk24-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk25-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk26-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk27-u9761b6bf4e/files/invalid_shard.shard", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/chnk28-u9761b6bf4e/files/invalid_shard.shard" ], "valid_reads": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/chnk0-u9761b69f72/files/valid.shard" ] }, "waiting": false }, { "id": "feature_counts", "type": "fbc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/join-u9761b69f68/files/feature_counts.fbc.bincode", "waiting": false }, { "id": "feature_reference", "type": "frf.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9761b69f68/files/feature_reference.frf.bincode", "waiting": false }, { "id": "target_set", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "chemistry_def", "type": "ChemistryDef", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": { "barcode": [ { "kind": "gel_bead", "length": 16, "offset": 0, "read_type": "R1", "whitelist": "737K-arc-v1" } ], "description": "Single Cell Multiome ATAC + Gene Expression v1", "endedness": "three_prime", "name": "ARC-v1", "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" } }, "waiting": false }, { "id": "include_introns", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "aligner", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "is_pd", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false }, { "id": "trim_polya_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "trim_tso_min_score", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 20, "waiting": false }, { "id": "total_barcode_counts", "type": "tbcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/total_barcode_counts.tbcc.bincode", "waiting": false }, { "id": "corrected_barcode_counts", "type": "bcc.bincode", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/BARCODE_CORRECTION/fork0/join-u9761b6bf4d/files/correct_barcode_counts.bcc.bincode", "waiting": false } ], "Return": null } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.BARCODE_CORRECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_READ_SHARDS_STRUCT", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.MAKE_SHARD", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER._SLFE_PARTIAL_FIRST_PASS" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "_JOINT_CELL_DETECTOR", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "rna_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "atac_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix.h5", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "force_cells", "type": "map\u003cMinCounts\u003e", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "rna_gem_groups", "type": "int[]", "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "waiting": false }, { "id": "disable_bc_multiplets", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false } ], "Return": [ { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "atac_cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/atac_formatted_cell_barcodes.csv", "waiting": false }, { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/singlecell.csv", "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-u9761b6d563/files/merged_summary.json", "waiting": false }, { "id": "excluded_barcodes", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u9761b6d527/files/excluded_barcodes.json", "waiting": false }, { "id": "atac_singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-u9761b6d563/files/atac_singlecell.csv", "waiting": false }, { "id": "rna_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u9761b6d563/files/summary.json", "waiting": false }, { "id": "joint_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix.h5", "waiting": false }, { "id": "filtered_matrix", "type": "AnalysisH5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5" }, "waiting": false }, { "id": "joint_raw_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix_mex", "waiting": false }, { "id": "joint_filtered_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_filtered_matrix_mex", "waiting": false }, { "id": "is_multi_genome", "type": "bool", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": false, "waiting": false }, { "id": "skip_analysis", "type": "bool", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": false, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "DETECT_JOINT_CELL_BARCODES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 6, "__vmem_gb": 9 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "rna_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "atac_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix.h5", "waiting": false }, { "id": "force_cells", "type": "map\u003cMinCounts\u003e", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "atac_excluded_bcs", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u9761b6d527/files/excluded_barcodes.json", "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/summary.json", "waiting": false }, { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/singlecell.csv", "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "atac_formatted_cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/atac_formatted_cell_barcodes.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/detect_joint_cell_barcodes" }, { "name": "FILTER_PEAK_MATRIX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3, "__vmem_gb": 6 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "num_analysis_bcs", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/atac_formatted_cell_barcodes.csv", "waiting": false }, { "id": "raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix.h5", "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join-u9761b6d563/files/filtered_matrix.h5", "waiting": false }, { "id": "filtered_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join-u9761b6d563/files/filtered_matrix_mex", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/filter_peak_matrix" }, { "name": "FILTER_UMI_MATRIX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "rna_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/cell_barcodes.csv", "waiting": false }, { "id": "gem_groups", "type": "int[]", "mode": "", "node": null, "matchedFork": null, "value": [ 1 ], "waiting": false } ], "Return": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u9761b6d563/files/filtered_matrix.h5", "waiting": false }, { "id": "filtered_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u9761b6d563/files/filtered_matrix_mex", "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u9761b6d563/files/summary.json", "waiting": false }, { "id": "is_multi_genome", "type": "bool", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": false, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/filter_umi_matrix" }, { "name": "GENERATE_SC_ATAC_COUNTS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 6, "__vmem_gb": 9 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr2" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr3" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr4" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr5" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr6" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr7" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chrX" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr8" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr9" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr11" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr10" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr12" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr13" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr14" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr15" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr16" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr17" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr18" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr20" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr19" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chrY", "KI270713.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr22", "KI270711.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "chr21", "KI270726.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "KI270728.1", "KI270721.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "KI270727.1", "KI270731.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "GL000009.2", "GL000218.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "GL000194.1", "GL000213.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "GL000205.2", "KI270734.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 6, "__threads": 1, "__vmem_gb": 9, "contigs": [ "GL000195.1", "GL000219.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/atac_formatted_cell_barcodes.csv", "waiting": false }, { "id": "excluded_barcodes", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u9761b6d527/files/excluded_barcodes.json", "waiting": false } ], "Return": [ { "id": "atac_singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-u9761b6d563/files/atac_singlecell.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/generate_sc_atac_counts" }, { "name": "MERGE_ATAC_RNA_MATRICES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3, "__vmem_gb": 6 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "atac_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.GENERATE_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u9761b6d34b/files/raw_matrix.h5", "waiting": false }, { "id": "atac_filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join-u9761b6d563/files/filtered_matrix.h5", "waiting": false }, { "id": "rna_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER.WRITE_H5_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u9761b6d4fd/files/raw_feature_bc_matrix.h5", "waiting": false }, { "id": "rna_filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u9761b6d563/files/filtered_matrix.h5", "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER.GEX_SETUP_CHUNKS", "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false } ], "Return": [ { "id": "joint_raw_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix.h5", "waiting": false }, { "id": "filtered_matrix", "type": "AnalysisH5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5" }, "waiting": false }, { "id": "joint_raw_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_raw_matrix_mex", "waiting": false }, { "id": "joint_filtered_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/joint_filtered_matrix_mex", "waiting": false }, { "id": "skip_analysis", "type": "bool", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": false, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._FASTQ_STAGER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._GEX_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_PEAK_MATRIX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.FILTER_UMI_MATRIX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/processing/merge_atac_rna_matrices" }, { "name": "MERGE_CELL_METRICS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "summary_jsons", "type": "json[]", "mode": "", "node": null, "matchedFork": null, "value": [ "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/low_targeting_summary.json", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-u9761b6d3f8/files/gel_bead_doublet_summary.json", null, "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/summary.json" ], "waiting": false } ], "Return": [ { "id": "merged_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-u9761b6d563/files/merged_summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_CELL_METRICS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/merge_summary_metrics" }, { "name": "MERGE_EXCLUDED_BARCODES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "barcode_exclusions", "type": "json[]", "mode": "", "node": null, "matchedFork": null, "value": [ null, "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-u9761b6d3f8/files/gel_bead_doublet_barcodes.json", "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/low_targeting_barcodes.json" ], "waiting": false } ], "Return": [ { "id": "excluded_barcodes", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u9761b6d527/files/excluded_barcodes.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/merge_excluded_barcodes" }, { "name": "REMOVE_BARCODE_MULTIPLETS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS", "state": "disabled", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "disabled", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS/fork0", "names": [ "disabled", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_BARCODE_MULTIPLETS/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/barcode_counts.json", "waiting": false } ], "Return": null } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_BARCODE_MULTIPLETS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/remove_barcode_multiplets" }, { "name": "REMOVE_GEL_BEAD_DOUBLET_BARCODES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr2" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr3" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr4" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr5" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr6" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr7" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chrX" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr8" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr9" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr11" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr10" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr12" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr13" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr14" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr15" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr16" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr17" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr18" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr20" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr19" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chrY", "KI270713.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr22", "KI270711.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "chr21", "KI270726.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "KI270728.1", "KI270721.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "KI270727.1", "KI270731.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "GL000009.2", "GL000218.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "GL000194.1", "GL000213.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "GL000205.2", "KI270734.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "contigs": [ "GL000195.1", "GL000219.1" ], "valid_barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/split-u9761b6d3f8/files/valid_barcodes.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/barcode_counts.json", "waiting": false } ], "Return": [ { "id": "gel_bead_doublet_barcodes", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-u9761b6d3f8/files/gel_bead_doublet_barcodes.json", "waiting": false }, { "id": "gel_bead_doublet_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-u9761b6d3f8/files/gel_bead_doublet_summary.json", "waiting": false }, { "id": "connect_matrix", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_GEL_BEAD_DOUBLET_BARCODES/fork0/join-u9761b6d3f8/files/connect_matrix.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_GEL_BEAD_DOUBLET_BARCODES" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/remove_gel_bead_doublet_barcodes" }, { "name": "REMOVE_LOW_TARGETING_BARCODES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr2" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr3" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr4" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr5" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr6" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr7" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chrX" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr8" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr9" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr11" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr10" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr12" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr13" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr14" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr15" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr16" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr17" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr18" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr20" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr19" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chrY", "KI270713.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr22", "KI270711.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "chr21", "KI270726.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "KI270728.1", "KI270721.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "KI270727.1", "KI270731.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "GL000009.2", "GL000218.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "GL000194.1", "GL000213.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "GL000205.2", "KI270734.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 2, "__threads": 1, "__vmem_gb": 5, "contigs": [ "GL000195.1", "GL000219.1" ] }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false } ], "Return": [ { "id": "barcode_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/barcode_counts.json", "waiting": false }, { "id": "low_targeting_barcodes", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/low_targeting_barcodes.json", "waiting": false }, { "id": "low_targeting_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/low_targeting_summary.json", "waiting": false }, { "id": "fragment_lengths", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/fragment_lengths.json", "waiting": false }, { "id": "covered_bases", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/REMOVE_LOW_TARGETING_BARCODES/fork0/join-u9761b6d34b/files/covered_bases.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.REMOVE_LOW_TARGETING_BARCODES" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/processing/cell_calling/remove_low_targeting_barcodes" }, { "name": "_SC_ATAC_GEX_ANALYZER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "matrix", "type": "AnalysisH5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5" }, "waiting": false }, { "id": "method", "type": "AnalysisString", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "lsa", "atac_gex": "pca", "gex": "pca" }, "waiting": false }, { "id": "projection_dims", "type": "AnalysisInt", "mode": "", "node": null, "matchedFork": null, "value": { "atac": 15, "atac_gex": 15, "gex": 10 }, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "feature_linkage_max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "linkage_projection", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "analysis_csv", "type": "AnalysisOutput", "mode": "", "node": null, "matchedFork": null, "value": { "clustering": { "atac": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } }, "gex": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } } }, "dimensionality_reduction": { "atac": { "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/projection.csv", "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/components.csv", "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv", "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/variance.csv", "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_umap_csv/2_components/projection.csv" }, "gex": { "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "pca_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/components.csv", "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/dispersion.csv", "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/variance.csv", "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_umap_csv/2_components/projection.csv" } }, "feature_linkage": { "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage.bedpe", "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage_matrix.h5" }, "tf_analysis": { "filtered_tf_bc_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix_mex", "filtered_tf_bc_matrix_h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "peak_motif_mapping": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u9761b6d667/files/peak_motif_hits.bed" } }, "waiting": false }, { "id": "analysis_h5", "type": "h5", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u9761b6d784/files/analysis_h5.h5", "waiting": false }, { "id": "peak_annotation", "type": "tsv", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false }, { "id": "is_multi_genome", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "loupe_matrix_h5", "type": "h5", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u9761b6d784/files/loupe_matrix_h5.h5", "waiting": false }, { "id": "summary", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ATAC_GEX_SUMMARIZE_ANALYSIS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 5, "__vmem_gb": 8 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "matrix", "type": "AnalysisH5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5" }, "waiting": false }, { "id": "tf_propZ_matrix", "type": "gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/tf_propZ_matrix.gz", "waiting": false }, { "id": "peak_annotation", "type": "tsv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false }, { "id": "reduced_data", "type": "ProjectionOutputMap", "mode": "", "node": null, "matchedFork": null, "value": { "atac": { "method": "lsa", "num_dims": 15, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" }, "atac_gex": null, "gex": { "method": "pca", "num_dims": 10, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" } }, "waiting": false }, { "id": "tsne", "type": "AnalysisPath", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output", "atac_gex": null, "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output" }, "waiting": false }, { "id": "umap", "type": "AnalysisPath", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output", "atac_gex": null, "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output" }, "waiting": false }, { "id": "clustering", "type": "AnalysisPath", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering", "atac_gex": null, "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering" }, "waiting": false }, { "id": "differential_expression", "type": "GexDeCluster", "mode": "", "node": null, "matchedFork": null, "value": { "atac": { "csv": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv", "h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_h5.h5" }, "atac_gex": null, "gex": { "csv": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv", "h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_h5.h5" } }, "waiting": false }, { "id": "differential_accessibility", "type": "AnalysisPath", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis", "atac_gex": null, "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis" }, "waiting": false }, { "id": "filtered_tf_bc_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "waiting": false }, { "id": "max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "feature_linkage", "type": "FeatureLinkageOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES", "matchedFork": null, "value": { "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage.bedpe", "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage_matrix.h5" }, "waiting": false } ], "Return": [ { "id": "clustering_output", "type": "ClusteringOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS", "matchedFork": null, "value": { "atac": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/lsa/lsa_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } }, "gex": { "graphclust": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/graphclust/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/graphclust/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/graphclust/differential_expression.csv" }, "kmeans_2_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_2_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_2_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_2_clusters/differential_expression.csv" }, "kmeans_3_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_3_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_3_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_3_clusters/differential_expression.csv" }, "kmeans_4_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_4_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_4_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_4_clusters/differential_expression.csv" }, "kmeans_5_clusters": { "clusters": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_csv/kmeans_5_clusters/clusters.csv", "differential_expression": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv/kmeans_5_clusters/differential_expression.csv", "differential_accessibility": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis/pca/pca_enrichment_csv/kmeans_5_clusters/differential_expression.csv" } } }, "waiting": false }, { "id": "dr_output", "type": "DimensionReductionOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS", "matchedFork": null, "value": { "atac": { "lsa_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/projection.csv", "lsa_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/components.csv", "lsa_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/dispersion.csv", "lsa_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/variance.csv", "lsa_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/lsa/lsa_csv/15_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output/lsa_umap_csv/2_components/projection.csv" }, "gex": { "pca_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "pca_components": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/components.csv", "pca_dispersion": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/dispersion.csv", "pca_variance": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/variance.csv", "pca_features_selected": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/features_selected.csv", "tsne_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_tsne_csv/2_components/projection.csv", "umap_projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output/pca_umap_csv/2_components/projection.csv" } }, "waiting": false }, { "id": "analysis_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u9761b6d784/files/analysis_h5.h5", "waiting": false }, { "id": "loupe_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u9761b6d784/files/loupe_matrix_h5.h5", "waiting": false }, { "id": "is_multi_genome", "type": "bool", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS", "matchedFork": null, "value": false, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.ATAC_GEX_SUMMARIZE_ANALYSIS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/analyzer/atac_gex_summarize_analysis" }, { "name": "PARSE_REDUCED_DIM", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/PARSE_REDUCED_DIM/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "linkage_projection", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "reduced_data", "type": "ProjectionOutputMap", "mode": "", "node": null, "matchedFork": null, "value": { "atac": { "method": "lsa", "num_dims": 15, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" }, "atac_gex": null, "gex": { "method": "pca", "num_dims": 10, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" } }, "waiting": false }, { "id": "matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5", "waiting": false } ], "Return": [ { "id": "reduced_dim_projection", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/analyzer/parse_reduced_dim" }, { "name": "_ATAC_CLUSTERING_COMPUTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "reduced_data", "type": "ProjectionOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": { "method": "lsa", "num_dims": 15, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" }, "waiting": false }, { "id": "matrix_clustering", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "matrix", "type": "AnalysisH5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5" }, "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "filtered_tf_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "waiting": false }, { "id": "neighbor_a", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "neighbor_b", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "graphclust_neighbors", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "clustering", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering", "waiting": false }, { "id": "enrichment_atac", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis", "waiting": false }, { "id": "enrichment_gex", "type": "GexDe", "mode": "", "node": null, "matchedFork": null, "value": { "csv": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv", "h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_h5.h5" }, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ATAC_RUN_GRAPH_CLUSTERING", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3, "__vmem_gb": 6 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "k_nearest": 130, "method": "lsa", "neighbor_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-u9761b6d679/files/neighbor_index_lsa.pickle", "row_start": 0, "submatrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-u9761b6d679/files/lsa_0_submatrix.h5", "total_rows": 1007, "use_bcs": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-u9761b6d679/files/use_bcs.h5" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "lsa" ], "waiting": false }, { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false }, { "id": "num_neighbors", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "neighbor_a", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "neighbor_b", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "balltree_leaf_size", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "similarity_type", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "nn", "waiting": false } ], "Return": [ { "id": "chunked_neighbors", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "matchedFork": null, "value": null, "waiting": false }, { "id": "knn_clusters", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-u9761b6d679/files/knn_clusters", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_graph_clustering" }, { "name": "CLUSTER_CELLS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 2 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 3 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk2", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 5 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk3", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "lsa" ], "waiting": false }, { "id": "minclusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 2, "waiting": false }, { "id": "maxclusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "num_dims", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "clustered_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-u9761b6d679/files/clustered_data", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/cluster_cells" }, { "name": "COMBINE_CLUSTERING", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "clustered_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-u9761b6d679/files/clustered_data", "waiting": false }, { "id": "knn_clusters", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-u9761b6d679/files/knn_clusters", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "lsa" ], "waiting": false } ], "Return": [ { "id": "clustering", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering", "waiting": false }, { "id": "clustering_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_clustering.h5", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.CLUSTER_CELLS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/combine_clustering" }, { "name": "COMPUTE_DIFFERENTIAL_ATAC", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 0.7626953125, "__vmem_gb": 3.7626953125 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "graphclust", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "graphclust", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "graphclust", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 4, "clustering_key": "graphclust", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 5, "clustering_key": "graphclust", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_2_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_2_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_3_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_3_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "kmeans_3_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_4_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_4_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "kmeans_4_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 4, "clustering_key": "kmeans_4_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_5_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_5_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "kmeans_5_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 4, "clustering_key": "kmeans_5_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 5, "clustering_key": "kmeans_5_clusters", "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "filtered_peak_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "filtered_tf_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "lsa" ], "waiting": false }, { "id": "clustering", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering", "waiting": false } ], "Return": [ { "id": "enrichment_analysis", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/perform_differential_analysis" }, { "name": "COMPUTE_DIFFERENTIAL_GEX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "graphclust" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_2_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_3_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk2", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_4_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk3", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_5_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk4", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "clustering_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d686/files/clustering/lsa/lsa_clustering.h5", "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "is_antibody_only", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "skip", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false } ], "Return": [ { "id": "diffexp_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_h5.h5", "waiting": false }, { "id": "diffexp_csv", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d687/files/diffexp_csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._ATAC_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/analyzer/run_differential_expression" }, { "name": "_DIMENSION_REDUCER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "matrix", "type": "AnalysisH5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5" }, "waiting": false }, { "id": "method", "type": "AnalysisString", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "lsa", "atac_gex": "pca", "gex": "pca" }, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "projection_dims", "type": "AnalysisInt", "mode": "", "node": null, "matchedFork": null, "value": { "atac": 15, "atac_gex": 15, "gex": 10 }, "waiting": false } ], "Return": [ { "id": "reduced_data", "type": "ProjectionOutputMap", "mode": "", "node": null, "matchedFork": null, "value": { "atac": { "method": "lsa", "num_dims": 15, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" }, "atac_gex": null, "gex": { "method": "pca", "num_dims": 10, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" } }, "waiting": false }, { "id": "tsne", "type": "AnalysisPath", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output", "atac_gex": null, "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output" }, "waiting": false }, { "id": "umap", "type": "AnalysisPath", "mode": "", "node": null, "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output", "atac_gex": null, "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output" }, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "_ATAC_DIMENSION_REDUCER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "method", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "lsa", "waiting": false }, { "id": "num_dims", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 15, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "reduced_data", "type": "ProjectionOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": { "method": "lsa", "num_dims": 15, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" }, "waiting": false }, { "id": "tsne", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output", "waiting": false }, { "id": "umap", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "REDUCE_DIMENSIONS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 13, "method": "lsa" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "lsa" ], "waiting": false }, { "id": "num_dims", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 15, "waiting": false }, { "id": "num_bcs", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "num_features", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/reduce_dimensions" }, { "name": "RUN_MANIFOLD_PROJECTION", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 9, "method": "lsa", "projection": "tsne", "projection_dims": 2 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 3, "__threads": 4, "__vmem_gb": 9, "method": "lsa", "projection": "umap", "projection_dims": 2 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false }, { "id": "params", "type": "ManifoldParams", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "lsa" ], "waiting": false }, { "id": "projections", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "tsne", "umap" ], "waiting": false } ], "Return": [ { "id": "projection_output", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_ATAC_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d679/files/projection_output", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._ATAC_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_manifold_projection" }, { "name": "_GEX_DIMENSION_REDUCER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "method", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "pca", "waiting": false }, { "id": "num_dims", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 10, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "reduced_data", "type": "ProjectionOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": { "method": "pca", "num_dims": 10, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" }, "waiting": false }, { "id": "tsne", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output", "waiting": false }, { "id": "umap", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "REDUCE_DIMENSIONS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 13, "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "pca" ], "waiting": false }, { "id": "num_dims", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 10, "waiting": false }, { "id": "num_bcs", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "num_features", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/reduce_dimensions" }, { "name": "RUN_MANIFOLD_PROJECTION", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 9, "method": "pca", "projection": "tsne", "projection_dims": 2 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 3, "__threads": 4, "__vmem_gb": 9, "method": "pca", "projection": "umap", "projection_dims": 2 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false }, { "id": "params", "type": "ManifoldParams", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "pca" ], "waiting": false }, { "id": "projections", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "tsne", "umap" ], "waiting": false } ], "Return": [ { "id": "projection_output", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/RUN_MANIFOLD_PROJECTION/fork0/join-u9761b6d65e/files/projection_output", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.RUN_MANIFOLD_PROJECTION" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_manifold_projection" }, { "name": "_FEATURE_LINKAGE_COMPUTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "merged_filtered_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5", "waiting": false }, { "id": "reduced_dim_projection", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "waiting": false }, { "id": "atac_peak_annotation", "type": "tsv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "feature_linkage", "type": "FeatureLinkageOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES", "matchedFork": null, "value": { "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage.bedpe", "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage_matrix.h5" }, "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "COMPUTE_FEATURE_LINKAGES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1.5419921875, "__vmem_gb": 4.5419921875 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 2.29, "__threads": 1, "__vmem_gb": 5.29, "chunk_end": 58, "chunk_start": 0 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 2.19, "__threads": 1, "__vmem_gb": 5.19, "chunk_end": 116, "chunk_start": 58 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 2.23, "__threads": 1, "__vmem_gb": 5.23, "chunk_end": 174, "chunk_start": 116 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 2.22, "__threads": 1, "__vmem_gb": 5.22, "chunk_end": 232, "chunk_start": 174 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 2.19, "__threads": 1, "__vmem_gb": 5.19, "chunk_end": 291, "chunk_start": 232 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 2.21, "__threads": 1, "__vmem_gb": 5.21, "chunk_end": 349, "chunk_start": 291 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 2.21, "__threads": 1, "__vmem_gb": 5.21, "chunk_end": 407, "chunk_start": 349 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 2.24, "__threads": 1, "__vmem_gb": 5.24, "chunk_end": 465, "chunk_start": 407 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 2.23, "__threads": 1, "__vmem_gb": 5.23, "chunk_end": 524, "chunk_start": 465 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 2.21, "__threads": 1, "__vmem_gb": 5.21, "chunk_end": 582, "chunk_start": 524 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 2.23, "__threads": 1, "__vmem_gb": 5.23, "chunk_end": 640, "chunk_start": 582 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 2.17, "__threads": 1, "__vmem_gb": 5.17, "chunk_end": 698, "chunk_start": 640 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 2.19, "__threads": 1, "__vmem_gb": 5.19, "chunk_end": 757, "chunk_start": 698 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 2.24, "__threads": 1, "__vmem_gb": 5.24, "chunk_end": 815, "chunk_start": 757 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 2.23, "__threads": 1, "__vmem_gb": 5.23, "chunk_end": 873, "chunk_start": 815 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 2.26, "__threads": 1, "__vmem_gb": 5.26, "chunk_end": 931, "chunk_start": 873 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 2.25, "__threads": 1, "__vmem_gb": 5.25, "chunk_end": 990, "chunk_start": 931 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 2.28, "__threads": 1, "__vmem_gb": 5.28, "chunk_end": 1048, "chunk_start": 990 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 2.22, "__threads": 1, "__vmem_gb": 5.22, "chunk_end": 1106, "chunk_start": 1048 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 2.27, "__threads": 1, "__vmem_gb": 5.27, "chunk_end": 1164, "chunk_start": 1106 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "__mem_gb": 2.32, "__threads": 1, "__vmem_gb": 5.32, "chunk_end": 1223, "chunk_start": 1164 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "__mem_gb": 2.2, "__threads": 1, "__vmem_gb": 5.2, "chunk_end": 1281, "chunk_start": 1223 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "__mem_gb": 2.18, "__threads": 1, "__vmem_gb": 5.18, "chunk_end": 1339, "chunk_start": 1281 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "__mem_gb": 2.18, "__threads": 1, "__vmem_gb": 5.18, "chunk_end": 1397, "chunk_start": 1339 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 24, "chunkDef": { "__mem_gb": 2.21, "__threads": 1, "__vmem_gb": 5.21, "chunk_end": 1456, "chunk_start": 1397 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk24", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 25, "chunkDef": { "__mem_gb": 2.22, "__threads": 1, "__vmem_gb": 5.22, "chunk_end": 1514, "chunk_start": 1456 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk25", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 26, "chunkDef": { "__mem_gb": 2.26, "__threads": 1, "__vmem_gb": 5.26, "chunk_end": 1572, "chunk_start": 1514 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk26", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 27, "chunkDef": { "__mem_gb": 2.22, "__threads": 1, "__vmem_gb": 5.22, "chunk_end": 1630, "chunk_start": 1572 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk27", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 28, "chunkDef": { "__mem_gb": 2.17, "__threads": 1, "__vmem_gb": 5.17, "chunk_end": 1688, "chunk_start": 1630 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk28", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 29, "chunkDef": { "__mem_gb": 2.2, "__threads": 1, "__vmem_gb": 5.2, "chunk_end": 1747, "chunk_start": 1688 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk29", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 30, "chunkDef": { "__mem_gb": 2.2, "__threads": 1, "__vmem_gb": 5.2, "chunk_end": 1805, "chunk_start": 1747 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk30", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 31, "chunkDef": { "__mem_gb": 2.18, "__threads": 1, "__vmem_gb": 5.18, "chunk_end": 1863, "chunk_start": 1805 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk31", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 32, "chunkDef": { "__mem_gb": 2.16, "__threads": 1, "__vmem_gb": 5.16, "chunk_end": 1921, "chunk_start": 1863 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk32", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 33, "chunkDef": { "__mem_gb": 2.17, "__threads": 1, "__vmem_gb": 5.17, "chunk_end": 1980, "chunk_start": 1921 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk33", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 34, "chunkDef": { "__mem_gb": 2.18, "__threads": 1, "__vmem_gb": 5.18, "chunk_end": 2038, "chunk_start": 1980 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk34", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 35, "chunkDef": { "__mem_gb": 2.17, "__threads": 1, "__vmem_gb": 5.17, "chunk_end": 2096, "chunk_start": 2038 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk35", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 36, "chunkDef": { "__mem_gb": 2.23, "__threads": 1, "__vmem_gb": 5.23, "chunk_end": 2154, "chunk_start": 2096 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk36", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 37, "chunkDef": { "__mem_gb": 2.23, "__threads": 1, "__vmem_gb": 5.23, "chunk_end": 2213, "chunk_start": 2154 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk37", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 38, "chunkDef": { "__mem_gb": 2.17, "__threads": 1, "__vmem_gb": 5.17, "chunk_end": 2271, "chunk_start": 2213 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk38", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 39, "chunkDef": { "__mem_gb": 2.21, "__threads": 1, "__vmem_gb": 5.21, "chunk_end": 2329, "chunk_start": 2271 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk39", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 40, "chunkDef": { "__mem_gb": 2.2, "__threads": 1, "__vmem_gb": 5.2, "chunk_end": 2387, "chunk_start": 2329 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk40", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 41, "chunkDef": { "__mem_gb": 2.19, "__threads": 1, "__vmem_gb": 5.19, "chunk_end": 2446, "chunk_start": 2387 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk41", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 42, "chunkDef": { "__mem_gb": 2.22, "__threads": 1, "__vmem_gb": 5.22, "chunk_end": 2504, "chunk_start": 2446 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk42", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 43, "chunkDef": { "__mem_gb": 2.18, "__threads": 1, "__vmem_gb": 5.18, "chunk_end": 2562, "chunk_start": 2504 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk43", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 44, "chunkDef": { "__mem_gb": 2.19, "__threads": 1, "__vmem_gb": 5.19, "chunk_end": 2620, "chunk_start": 2562 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk44", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 45, "chunkDef": { "__mem_gb": 2.17, "__threads": 1, "__vmem_gb": 5.17, "chunk_end": 2679, "chunk_start": 2620 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk45", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 46, "chunkDef": { "__mem_gb": 2.24, "__threads": 1, "__vmem_gb": 5.24, "chunk_end": 2737, "chunk_start": 2679 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk46", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 47, "chunkDef": { "__mem_gb": 2.17, "__threads": 1, "__vmem_gb": 5.17, "chunk_end": 2795, "chunk_start": 2737 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk47", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 48, "chunkDef": { "__mem_gb": 2.15, "__threads": 1, "__vmem_gb": 5.15, "chunk_end": 2853, "chunk_start": 2795 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk48", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 49, "chunkDef": { "__mem_gb": 2.15, "__threads": 1, "__vmem_gb": 5.15, "chunk_end": 2912, "chunk_start": 2853 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/chnk49", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "merged_filtered_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5", "waiting": false }, { "id": "atac_peak_annotation", "type": "tsv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_metadata", "type": "BarcodeMetadata", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX", "matchedFork": null, "value": { "smoothing_weights": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/smoothing_weights.h5", "similarity_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/similarity_matrix.h5", "depth_scale_factors": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/depth_scale_factors.csv" }, "waiting": false }, { "id": "feature_grouping", "type": "pkl", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/feature_grouping.pkl", "waiting": false }, { "id": "max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "feature_linkage", "type": "FeatureLinkageOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES", "matchedFork": null, "value": { "feature_linkage": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage.bedpe", "feature_linkage_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/feature_linkage_matrix.h5" }, "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u9761b6d69b/files/summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.COMPUTE_FEATURE_LINKAGES" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/feature_linkage/compute_feature_linkages" }, { "name": "PREPROCESS_JOINT_MATRIX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 2, "__vmem_gb": 5 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "merged_filtered_matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5", "waiting": false }, { "id": "reduced_dim_projection", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data/pca/pca_csv/10_components/projection.csv", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "max_dist_mb", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "barcode_metadata", "type": "BarcodeMetadata", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX", "matchedFork": null, "value": { "smoothing_weights": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/smoothing_weights.h5", "similarity_matrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/similarity_matrix.h5", "depth_scale_factors": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/depth_scale_factors.csv" }, "waiting": false }, { "id": "feature_grouping", "type": "pkl", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/PREPROCESS_JOINT_MATRIX/fork0/join-u9761b6d67b/files/feature_grouping.pkl", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER.PARSE_REDUCED_DIM", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._FEATURE_LINKAGE_COMPUTER.PREPROCESS_JOINT_MATRIX" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac_rna/stages/feature_linkage/preprocess_joint_matrix" }, { "name": "_GEX_CLUSTERING_COMPUTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "reduced_data", "type": "ProjectionOutput", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": { "method": "pca", "num_dims": 10, "projection": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data" }, "waiting": false }, { "id": "matrix_clustering", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "matrix", "type": "AnalysisH5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": { "atac": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "atac_gex": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac_gex.h5" }, "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "filtered_tf_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "waiting": false }, { "id": "neighbor_a", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "neighbor_b", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "graphclust_neighbors", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "clustering", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering", "waiting": false }, { "id": "enrichment_atac", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis", "waiting": false }, { "id": "enrichment_gex", "type": "GexDe", "mode": "", "node": null, "matchedFork": null, "value": { "csv": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv", "h5": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_h5.h5" }, "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ATAC_RUN_GRAPH_CLUSTERING", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3, "__vmem_gb": 6 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4, "k_nearest": 130, "method": "pca", "neighbor_index": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-u9761b6d65e/files/neighbor_index_pca.pickle", "row_start": 0, "submatrix": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-u9761b6d65e/files/pca_0_submatrix.h5", "total_rows": 1007, "use_bcs": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/split-u9761b6d65e/files/use_bcs.h5" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "pca" ], "waiting": false }, { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false }, { "id": "num_neighbors", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "neighbor_a", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "neighbor_b", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "balltree_leaf_size", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "similarity_type", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "nn", "waiting": false } ], "Return": [ { "id": "chunked_neighbors", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "matchedFork": null, "value": null, "waiting": false }, { "id": "knn_clusters", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-u9761b6d65e/files/knn_clusters", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/run_graph_clustering" }, { "name": "CLUSTER_CELLS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 2 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 3 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk2", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 5, "__threads": 1, "__vmem_gb": 8, "n_clusters": 5 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/chnk3", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "reduced_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER._GEX_DIMENSION_REDUCER.REDUCE_DIMENSIONS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_DIMENSION_REDUCER/_GEX_DIMENSION_REDUCER/REDUCE_DIMENSIONS/fork0/join-u9761b6d64e/files/reduced_data", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "pca" ], "waiting": false }, { "id": "minclusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": 2, "waiting": false }, { "id": "maxclusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "num_dims", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "clustered_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-u9761b6d65e/files/clustered_data", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/cluster_cells" }, { "name": "COMBINE_CLUSTERING", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "clustered_data", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/CLUSTER_CELLS/fork0/join-u9761b6d65e/files/clustered_data", "waiting": false }, { "id": "knn_clusters", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/ATAC_RUN_GRAPH_CLUSTERING/fork0/join-u9761b6d65e/files/knn_clusters", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "pca" ], "waiting": false } ], "Return": [ { "id": "clustering", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering", "waiting": false }, { "id": "clustering_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_clustering.h5", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.ATAC_RUN_GRAPH_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.CLUSTER_CELLS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/combine_clustering" }, { "name": "COMPUTE_DIFFERENTIAL_ATAC", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 0.7626953125, "__vmem_gb": 3.7626953125 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "graphclust", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "graphclust", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "graphclust", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 4, "clustering_key": "graphclust", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 5, "clustering_key": "graphclust", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_2_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_2_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_3_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_3_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "kmeans_3_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_4_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_4_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "kmeans_4_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 4, "clustering_key": "kmeans_4_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 1, "clustering_key": "kmeans_5_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 2, "clustering_key": "kmeans_5_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 3, "clustering_key": "kmeans_5_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 4, "clustering_key": "kmeans_5_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 1.18, "__threads": 4, "__vmem_gb": 4.18, "cluster": 5, "clustering_key": "kmeans_5_clusters", "method": "pca" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "filtered_peak_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "filtered_tf_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "waiting": false }, { "id": "factorization", "type": "string[]", "mode": "", "node": null, "matchedFork": null, "value": [ "pca" ], "waiting": false }, { "id": "clustering", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering", "waiting": false } ], "Return": [ { "id": "enrichment_analysis", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_ATAC/fork0/join-u9761b6d69d/files/enrichment_analysis", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._DIMENSION_REDUCER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_ATAC" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/perform_differential_analysis" }, { "name": "COMPUTE_DIFFERENTIAL_GEX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "graphclust" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_2_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk1", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_3_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk2", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_4_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk3", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 3, "__threads": 1, "__vmem_gb": 6, "clustering_key": "kmeans_5_clusters" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/chnk4", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "matrix_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/gex.h5", "waiting": false }, { "id": "clustering_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u9761b6d66d/files/clustering/pca/pca_clustering.h5", "waiting": false }, { "id": "random_seed", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "max_clusters", "type": "int", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "is_antibody_only", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "skip", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false } ], "Return": [ { "id": "diffexp_h5", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_h5.h5", "waiting": false }, { "id": "diffexp_csv", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_GEX_CLUSTERING_COMPUTER/COMPUTE_DIFFERENTIAL_GEX/fork0/join-u9761b6d677/files/diffexp_csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMBINE_CLUSTERING", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._GEX_CLUSTERING_COMPUTER.COMPUTE_DIFFERENTIAL_GEX" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/rna/stages/analyzer/run_differential_expression" }, { "name": "_PEAK_ANNOTATOR", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "filtered_peak_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "pwm_threshold", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "filtered_tf_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "waiting": false }, { "id": "filtered_tf_bc_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix_mex", "waiting": false }, { "id": "tf_propZ_matrix", "type": "gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/tf_propZ_matrix.gz", "waiting": false }, { "id": "peak_annotation", "type": "tsv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false }, { "id": "peak_motif_hits", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u9761b6d667/files/peak_motif_hits.bed", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "ANNOTATE_PEAKS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 5, "__vmem_gb": 8 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 2450, "chunk_start": 0, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 4901, "chunk_start": 2450, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 7352, "chunk_start": 4901, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 9803, "chunk_start": 7352, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 12254, "chunk_start": 9803, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 14705, "chunk_start": 12254, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 17156, "chunk_start": 14705, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 19607, "chunk_start": 17156, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 22058, "chunk_start": 19607, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 24509, "chunk_start": 22058, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 26959, "chunk_start": 24509, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 29410, "chunk_start": 26959, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 31861, "chunk_start": 29410, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 34312, "chunk_start": 31861, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 36763, "chunk_start": 34312, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 39214, "chunk_start": 36763, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 41665, "chunk_start": 39214, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 44116, "chunk_start": 41665, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 46567, "chunk_start": 44116, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "chunk_end": 49018, "chunk_start": 46567, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false } ], "Return": [ { "id": "peak_annotation", "type": "tsv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-u9761b6d64e/files/peak_annotation.tsv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/annotate_peaks" }, { "name": "COMPUTE_GC_DISTRIBUTION", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false } ], "Return": [ { "id": "GCdict", "type": "pickle", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/join-u9761b6d64e/files/GCdict.pickle", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/compute_gc_dist" }, { "name": "GENERATE_TF_MATRIX", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 3, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "filtered_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "peak_motif_hits", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u9761b6d667/files/peak_motif_hits.bed", "waiting": false } ], "Return": [ { "id": "filtered_tf_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix.h5", "waiting": false }, { "id": "filtered_tf_bc_matrix_mex", "type": "path", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/filtered_tf_bc_matrix_mex", "waiting": false }, { "id": "tf_propZ_matrix", "type": "gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u9761b6d68a/files/tf_propZ_matrix.gz", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.GENERATE_TF_MATRIX" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/generate_tf_matrix" }, { "name": "SCAN_MOTIFS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.2084726867335563_0.3710843373493976", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.3710843373493976_0.39148936170212767", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.39148936170212767_0.40561797752808987", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.40561797752808987_0.4178454842219804", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.4178454842219804_0.42788461538461536", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.42788461538461536_0.43719806763285024", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.43719806763285024_0.44653349001175086", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.44653349001175086_0.455456570155902", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.455456570155902_0.46467065868263474", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.46467065868263474_0.47385272145144075", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.47385272145144075_0.4835164835164835", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.4835164835164835_0.4938956714761376", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.4938956714761376_0.5053507728894173", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.5053507728894173_0.5189309576837416", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.5189309576837416_0.5334190231362468", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.5334190231362468_0.5502283105022832", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.5502283105022832_0.5677777777777778", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.5677777777777778_0.587088915956151", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.587088915956151_0.6068702290076335", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.6068702290076335_0.6275395033860045", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 20, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.6275395033860045_0.6485875706214689", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk20", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 21, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.6485875706214689_0.6716417910447762", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk21", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 22, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.6716417910447762_0.6975903614457831", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk22", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 23, "chunkDef": { "GCdict": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/split-u9761b6d667/files/GCdict_0.6975903614457831_0.8679012345679012", "__mem_gb": 8, "__threads": 1, "__vmem_gb": 13, "skip": false }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/chnk23", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "globalGCdict", "type": "pickle", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/COMPUTE_GC_DISTRIBUTION/fork0/join-u9761b6d64e/files/GCdict.pickle", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "pwm_threshold", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "peak_motif_hits", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u9761b6d667/files/peak_motif_hits.bed", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.COMPUTE_GC_DISTRIBUTION", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.SCAN_MOTIFS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/analysis/scan_motifs" }, { "name": "_SC_ATAC_METRIC_COLLECTOR", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "basic_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/summary.json", "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "singlecell_mapping", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/singlecell.csv", "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/atac_formatted_cell_barcodes.csv", "waiting": false }, { "id": "singlecell_cells", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-u9761b6d563/files/atac_singlecell.csv", "waiting": false }, { "id": "insert_sizes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/insert_sizes.csv", "waiting": false }, { "id": "frag_bc_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/frag_bc_counts.json", "waiting": false } ], "Return": [ { "id": "singlecell_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5fd/files/summary.json", "waiting": false }, { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5ec/files/singlecell.csv", "waiting": false }, { "id": "enrichment_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-u9761b6d53a/files/summary_metrics.json", "waiting": false }, { "id": "insert_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-u9761b6d0e6/files/insert_summary.json", "waiting": false }, { "id": "bulk_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/bulk_complexity.json", "waiting": false }, { "id": "singlecell_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/singlecell_complexity.json", "waiting": false }, { "id": "complexity_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/complexity_summary.json", "waiting": false }, { "id": "tss_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/tss.csv", "waiting": false }, { "id": "ctcf_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/ctcf.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "COMPUTE_FRAGMENT_METRICS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 4, "__mem_gb": 3, "__vmem_gb": 6 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [], "bindings": { "Argument": [ { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "fragments_index", "type": "tsv.gz.tbi", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz.tbi", "waiting": false }, { "id": "peaks", "type": "bed", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peaks.bed", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "targeting_only", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": true, "waiting": false } ], "Return": [ { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/singlecell.csv", "waiting": false }, { "id": "ctcf_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/ctcf.csv", "waiting": false }, { "id": "tss_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/tss.csv", "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": null, "waiting": false }, { "id": "frag_bc_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/frag_bc_counts.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS" } ], "stagecodeLang": "Compiled", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/lib/bin/cr_atac martian compute_fragment_metrics" }, { "name": "ESTIMATE_LIBRARY_COMPLEXITY", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split", "names": [ "args", "complete", "jobinfo", "log", "stage_defs", "stderr", "stdout" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join", "names": [ "args", "chunk_defs", "chunk_outs", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_0.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk00", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 1, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_1.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk01", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 2, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_2.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk02", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 3, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_3.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk03", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 4, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_4.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk04", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 5, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_5.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk05", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 6, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_6.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk06", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 7, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_7.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk07", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 8, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_8.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk08", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 9, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_9.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk09", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 10, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_10.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk10", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 11, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_11.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk11", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 12, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_12.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk12", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 13, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_13.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk13", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 14, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_14.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk14", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 15, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_15.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk15", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 16, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_16.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk16", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 17, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_17.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk17", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 18, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_18.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk18", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } }, { "index": 19, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7, "barcodes": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/split-u9761b6d563/files/barcode_19.txt" }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/chnk19", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "sequencing_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/summary.json", "waiting": false }, { "id": "fragments", "type": "tsv.gz", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/fragments.tsv.gz", "waiting": false }, { "id": "cell_barcodes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.DETECT_JOINT_CELL_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u9761b6d552/files/atac_formatted_cell_barcodes.csv", "waiting": false }, { "id": "frag_bc_counts", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/frag_bc_counts.json", "waiting": false } ], "Return": [ { "id": "bulk_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/bulk_complexity.json", "waiting": false }, { "id": "complexity_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/complexity_summary.json", "waiting": false }, { "id": "singlecell_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/singlecell_complexity.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/estimate_library_complexity" }, { "name": "MERGE_SINGLECELL_METRICS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 8, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 8, "__threads": 1, "__vmem_gb": 11 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "singlecell_mapping", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/singlecell.csv", "waiting": false }, { "id": "singlecell_cells", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.GENERATE_SC_ATAC_COUNTS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/GENERATE_SC_ATAC_COUNTS/fork0/join-u9761b6d563/files/atac_singlecell.csv", "waiting": false }, { "id": "singlecell_targets", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/singlecell.csv", "waiting": false } ], "Return": [ { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5ec/files/singlecell.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/merge_singlecell_metrics" }, { "name": "REPORT_INSERT_SIZES", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "insert_sizes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/insert_sizes.csv", "waiting": false } ], "Return": [ { "id": "insert_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-u9761b6d0e6/files/insert_summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/report_insert_sizes" }, { "name": "REPORT_TSS_CTCF", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 1, "__threads": 1, "__vmem_gb": 4 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "tss_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/tss.csv", "waiting": false }, { "id": "ctcf_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/ctcf.csv", "waiting": false } ], "Return": [ { "id": "summary_metrics", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-u9761b6d53a/files/summary_metrics.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/report_tss_ctcf" }, { "name": "SUMMARIZE_SINGLECELL_METRICS", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5ec/files/singlecell.csv", "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5fd/files/summary.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/metrics/summarize_singlecell_metrics" }, { "name": "_SC_ATAC_REPORTER", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER", "type": "pipeline", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": null, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/fork0/split", "names": [] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/fork0/join", "names": [] }, "chunks": [], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "peak_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peak_metrics.json", "waiting": false }, { "id": "cell_calling_summary", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "filtered_peak_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "excluded_barcodes", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u9761b6d527/files/excluded_barcodes.json", "waiting": false }, { "id": "bulk_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/bulk_complexity.json", "waiting": false }, { "id": "singlecell_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/singlecell_complexity.json", "waiting": false }, { "id": "complexity_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/complexity_summary.json", "waiting": false }, { "id": "basic_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/summary.json", "waiting": false }, { "id": "singlecell_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5fd/files/summary.json", "waiting": false }, { "id": "insert_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-u9761b6d0e6/files/insert_summary.json", "waiting": false }, { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5ec/files/singlecell.csv", "waiting": false }, { "id": "tss_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/tss.csv", "waiting": false }, { "id": "ctcf_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/ctcf.csv", "waiting": false }, { "id": "sc_insert_sizes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/insert_sizes.csv", "waiting": false }, { "id": "enrichment_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-u9761b6d53a/files/summary_metrics.json", "waiting": false }, { "id": "count_dict", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/count_dict.json", "waiting": false }, { "id": "analysis", "type": "h5", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/summary.json", "waiting": false }, { "id": "web_summary", "type": "html", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-u9761b6d77a/files/web_summary.html", "waiting": false }, { "id": "ws_data", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-u9761b6d77a/files/data.json", "waiting": false }, { "id": "summary_csv", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/summary_csv.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER" } ], "stagecodeLang": "", "stagecodeCmd": "" }, { "name": "CREATE_WEBSUMMARY", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 16, "__vmem_gb": 19 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 16, "__threads": 1, "__vmem_gb": 19 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "barcode_whitelist", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "737K-arc-v1", "waiting": false }, { "id": "singlecell", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.MERGE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5ec/files/singlecell.csv", "waiting": false }, { "id": "tss_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/tss.csv", "waiting": false }, { "id": "ctcf_relpos", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.COMPUTE_FRAGMENT_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/COMPUTE_FRAGMENT_METRICS/fork0/join-u9761b6d34b/files/ctcf.csv", "waiting": false }, { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_desc", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "sample_def", "type": "map[]", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "matchedFork": null, "value": [ { "fastq_id": null, "fastq_mode": "ILMN_BCL2FASTQ", "gem_group": null, "lanes": null, "library_type": "Chromatin Accessibility", "read_path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/scATAC/fastq", "sample_indices": [ "any" ], "sample_names": [ "samp24" ], "subsample_rate": null, "target_set": null, "target_set_name": null } ], "waiting": false }, { "id": "insert_sizes", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/insert_sizes.csv", "waiting": false }, { "id": "summary_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/summary.json", "waiting": false }, { "id": "bulk_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/bulk_complexity.json", "waiting": false }, { "id": "singlecell_complexity", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/singlecell_complexity.json", "waiting": false }, { "id": "analysis", "type": "h5", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "filtered_peak_bc_matrix", "type": "h5", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_ATAC_RNA_MATRICES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u9761b6d5a2/files/atac.h5", "waiting": false }, { "id": "excluded_barcodes", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR.MERGE_EXCLUDED_BARCODES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u9761b6d527/files/excluded_barcodes.json", "waiting": false }, { "id": "count_dict", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.COUNT_CUT_SITES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-u9761b6d0e6/files/count_dict.json", "waiting": false }, { "id": "debug", "type": "bool", "mode": "", "node": null, "matchedFork": null, "value": false, "waiting": false }, { "id": "peak_qval", "type": "float", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false } ], "Return": [ { "id": "web_summary", "type": "html", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-u9761b6d77a/files/web_summary.html", "waiting": false }, { "id": "data", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/CREATE_WEBSUMMARY/fork0/chnk0-u9761b6d77a/files/data.json", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER.SPLIT_SAMPLE_DEF", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._JOINT_CELL_DETECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.CREATE_WEBSUMMARY" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/reporter/create_websummary" }, { "name": "SUMMARIZE_REPORTS_SINGLECELL", "fqname": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "type": "stage", "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL", "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL", "names": [] }, "forks": [ { "index": 0, "argPermute": null, "joinDef": { "__threads": 1, "__mem_gb": 4, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0", "names": [ "complete", "invocation", "outs", "vdrkill" ] }, "split_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/split", "names": [ "args", "complete", "stage_defs" ] }, "join_metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/join", "names": [ "args", "chunk_defs", "complete", "outs" ] }, "chunks": [ { "index": 0, "chunkDef": { "__mem_gb": 4, "__threads": 1, "__vmem_gb": 7 }, "state": "complete", "metadata": { "path": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0", "names": [ "args", "complete", "jobinfo", "log", "outs", "stderr", "stdout" ] } } ], "bindings": { "Argument": [ { "id": "sample_id", "type": "string", "mode": "", "node": null, "matchedFork": null, "value": "samp24_CR_out", "waiting": false }, { "id": "reference_path", "type": "path", "mode": "", "node": null, "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/genome_annotations/refdata-cellranger-arc-GRCh38-2020-A-2.0.0", "waiting": false }, { "id": "complexity_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.ESTIMATE_LIBRARY_COMPLEXITY", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/ESTIMATE_LIBRARY_COMPLEXITY/fork0/join-u9761b6d563/files/complexity_summary.json", "waiting": false }, { "id": "cell_calling_summary", "type": "json", "mode": "", "node": null, "matchedFork": null, "value": null, "waiting": false }, { "id": "peak_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER._PEAK_CALLER.DETECT_PEAKS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u9761b6d137/files/peak_metrics.json", "waiting": false }, { "id": "basic_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER.MARK_ATAC_DUPLICATES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u9761b6cc1f/files/summary.json", "waiting": false }, { "id": "insert_summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_INSERT_SIZES", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_INSERT_SIZES/fork0/chnk0-u9761b6d0e6/files/insert_summary.json", "waiting": false }, { "id": "singlecell_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.SUMMARIZE_SINGLECELL_METRICS", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/SUMMARIZE_SINGLECELL_METRICS/fork0/chnk0-u9761b6d5fd/files/summary.json", "waiting": false }, { "id": "enrichment_results", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR.REPORT_TSS_CTCF", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/REPORT_TSS_CTCF/fork0/chnk0-u9761b6d53a/files/summary_metrics.json", "waiting": false } ], "Return": [ { "id": "analysis_params", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/analysis_params.json", "waiting": false }, { "id": "summary", "type": "json", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/summary.json", "waiting": false }, { "id": "summary_csv", "type": "csv", "mode": "reference", "node": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL", "matchedFork": null, "value": "/srv/scratch/ekotler/scMultiomics/samp24_20210520/samp24_CR_out/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u9761b6d779/files/summary_csv.csv", "waiting": false } ] } } ], "edges": [ { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._ATAC_MATRIX_COMPUTER", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL" }, { "from": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_METRIC_COLLECTOR", "to": "ID.samp24_CR_out.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_REPORTER.SUMMARIZE_REPORTS_SINGLECELL" } ], "stagecodeLang": "Python", "stagecodeCmd": "/users/ekotler/packages/cellranger-arc-2.0.0/mro/atac/stages/reporter/summarize_reports_singlecell" } ]