@include "atac/_atac_matrix_computer.mro"

call _ATAC_MATRIX_COMPUTER(
    chunks                 = [
        {
            barcode:           "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S2_L002_R2_001.fastq.gz",
            chemistry:         null,
            fastq_mode:        "ILMN_BCL2FASTQ",
            gem_group:         1,
            read1:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S2_L002_R1_001.fastq.gz",
            read2:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S2_L002_R3_001.fastq.gz",
            read_group:        "count-NYU070:MissingLibrary:1:HHCL3DRXY:2",
            reads_interleaved: false,
            sample_index:      "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S2_L002_I1_001.fastq.gz",
            subsample_rate:    1,
        },
        {
            barcode:           "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S3_L002_R2_001.fastq.gz",
            chemistry:         null,
            fastq_mode:        "ILMN_BCL2FASTQ",
            gem_group:         1,
            read1:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S3_L002_R1_001.fastq.gz",
            read2:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S3_L002_R3_001.fastq.gz",
            read_group:        "count-NYU070:MissingLibrary:1:HHCL3DRXY:2",
            reads_interleaved: false,
            sample_index:      "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S3_L002_I1_001.fastq.gz",
            subsample_rate:    1,
        },
        {
            barcode:           "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S4_L002_R2_001.fastq.gz",
            chemistry:         null,
            fastq_mode:        "ILMN_BCL2FASTQ",
            gem_group:         1,
            read1:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S4_L002_R1_001.fastq.gz",
            read2:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S4_L002_R3_001.fastq.gz",
            read_group:        "count-NYU070:MissingLibrary:1:HHCL3DRXY:2",
            reads_interleaved: false,
            sample_index:      "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S4_L002_I1_001.fastq.gz",
            subsample_rate:    1,
        },
        {
            barcode:           "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S5_L002_R2_001.fastq.gz",
            chemistry:         null,
            fastq_mode:        "ILMN_BCL2FASTQ",
            gem_group:         1,
            read1:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S5_L002_R1_001.fastq.gz",
            read2:             "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S5_L002_R3_001.fastq.gz",
            read_group:        "count-NYU070:MissingLibrary:1:HHCL3DRXY:2",
            reads_interleaved: false,
            sample_index:      "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/fastq/NYU070_ATAC_S5_L002_I1_001.fastq.gz",
            subsample_rate:    1,
        },
    ],
    barcode_whitelist_path = "/gpfs/share/apps/cellranger/arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
    reference_path         = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    assay                  = "arc",
    custom_peaks           = null,
    peak_qval              = null,
    no_bam                 = false,
    sample_id              = "count-NYU070",
    sample_desc            = "count-NYU070",
)
