@include "rna/_slfe_cells_reporter.mro"

call _SLFE_CELLS_REPORTER as _CELLS_REPORTER(
    chemistry_defs            = {
        "Gene Expression": {
            barcode: [
                {
                    kind:      "gel_bead",
                    length:    16,
                    offset:    0,
                    read_type: "R1",
                    whitelist: {
                        name:                       "3M-february-2018_TRU",
                        part:                       null,
                        slide:                      null,
                        translation:                false,
                        translation_whitelist_path: null,
                    },
                },
            ],
            barcode_extraction: null,
            description:        "Single Cell 3' v3 (polyA)",
            endedness:          "three_prime",
            name:               "SC3Pv3-polyA",
            rna: {
                length:     null,
                min_length: null,
                offset:     0,
                read_type:  "R2",
            },
            rna2:               null,
            strandedness:       "+",
            umi: [
                {
                    length:     12,
                    min_length: 10,
                    offset:     16,
                    read_type:  "R1",
                    whitelist:  null,
                },
            ],
        },
    },
    reference_path            = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-GCA_001417965_1_Aiptasia_genome_1_1_genomic",
    recovered_cells           = {
        per_gem_well: null,
        per_sample:   null,
    },
    force_cells               = {
        per_gem_well: null,
        per_sample:   null,
    },
    slfe_feature_reference    = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u29f8cf6748/files/feature_reference.frf.bincode",
    target_panel_summary      = null,
    matrices_h5               = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u29f8cfca0b/files/raw_feature_bc_matrix.h5",
    read_chunks               = [
        {
            "chemistry": {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": {
                            "name": "3M-february-2018_TRU",
                            "part": null,
                            "slide": null,
                            "translation": false,
                            "translation_whitelist_path": null,
                        },
                    },
                ],
                "barcode_extraction": null,
                "description": "Single Cell 3' v3 (polyA)",
                "endedness": "three_prime",
                "name": "SC3Pv3-polyA",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": [
                    {
                        "length": 12,
                        "min_length": 10,
                        "offset": 16,
                        "read_type": "R1",
                        "whitelist": null,
                    },
                ],
            },
            "chunk_id": 0,
            "fastq_id": null,
            "fastqs": {
                "i1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_I1_001.fastq.gz",
                "i2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_I2_001.fastq.gz",
                "r1": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1/Peak_004_2reprep_S2_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "cellranger-Aiptasia-sym_reprep1:0:1:AAFJ277M5:1",
            "read_lengths": {},
            "subsample_rate": null,
            "umi_extractor": {
                "translators": [null],
            },
        },
    ],
    gem_well                  = 1,
    report_mol_inputs         = [
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u29f8cf69be/files/bc_umi_info.bui",
        "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u29f8cf69be/files/bc_umi_info.bui",
    ],
    matrix_computer_summary   = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u29f8cfca16/files/summary.json",
    barcode_summary           = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/join-u29f8cfca0b/files/barcode_summary.h5",
    filtered_barcodes         = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/filtered_barcodes.csv",
    per_probe_metrics         = null,
    filter_barcodes_summary   = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/summary.json",
    per_barcode_metrics       = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u29f8cfca0d/files/per_barcode_metrics.csv",
    include_introns           = true,
    filter_probes             = null,
    disable_ab_aggregate_detection = false,
    disable_high_occupancy_gem_detection = false,
    disable_subsampling       = false,
    multi_config_sha          = null,
    barcode_index             = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/join-u29f8cf69bd/files/barcode_index.bi.bincode",
    slide_serial_capture_area = null,
)
