@include "rna/_slfe_cells_reporter.mro"

call _SLFE_CELLS_REPORTER as _GEX_CELLS_REPORTER(
    reference_path          = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    recovered_cells         = 1000,
    force_cells             = null,
    slfe_feature_reference  = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u45960d708c/files/feature_reference.frf.bincode",
    target_panel_summary    = null,
    target_set_name         = null,
    matrices_h5             = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u45960dd236/files/raw_feature_bc_matrix.h5",
    read_chunks             = [
        {
            "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": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_S1_L001_I1_001.fastq.gz",
                "i2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_S1_L001_I2_001.fastq.gz",
                "r1": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_S1_L001_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_S1_L001_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "count-NYU070:0:1:HHCL3DRXY:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    gem_well                = 1,
    report_mol_inputs       = [
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u45960db803/files/bc_umi_info.bui",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u45960db803/files/bc_umi_info.bui",
    ],
    matrix_computer_summary = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u45960dd54b/files/summary.json",
    barcode_summary         = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u45960dd236/files/barcode_summary.h5",
    filtered_barcodes       = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u45960dea76/files/cell_barcodes.csv",
    filter_barcodes_summary = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u45960dea93/files/summary.json",
    per_barcode_metrics     = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u45960dd24f/files/per_barcode_metrics.csv",
    include_introns         = true,
    multi_config_sha        = null,
    barcode_index           = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u45960db7ff/files/barcode_index.bi.bincode",
)
