@include "atac/_cr_atac_stages.mro"

call ALIGN_ATAC_READS(
    reference_path         = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    shards                 = [
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0-u45960d708f/files/out.shard",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk1-u45960d708f/files/out.shard",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk2-u45960d708f/files/out.shard",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk3-u45960d708f/files/out.shard",
    ],
    chunk_chemistry_map    = [
        "3p;rev",
        "3p;rev",
        "3p;rev",
        "3p;rev",
    ],
    barcode_counts         = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u45960d708f/files/barcode_counts.bch.bincode",
    barcode_whitelist_path = "/gpfs/share/apps/cellranger/arc-2.0.0/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
    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,
        },
    ],
    assay                  = "arc",
    num_read_pairs         = 461993231,
)
