@include "atac/_cr_atac_stages.mro"

call MAKE_ATAC_SHARDS(
    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",
)
