@include "atac/_cr_atac_stages.mro"

call MAKE_ATAC_SHARDS(
    chunks                 = [
        {
            "barcode": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L001_R2_001.fastq.gz",
            "chemistry": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": 1,
            "read1": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L001_R1_001.fastq.gz",
            "read2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L001_R3_001.fastq.gz",
            "read_group": "pbmc_granulocyte_sorted_10k:MissingLibrary:1:HJ2W5DSXY:1",
            "reads_interleaved": false,
            "sample_index": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L001_I1_001.fastq.gz",
            "subsample_rate": 1,
        },
        {
            "barcode": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L002_R2_001.fastq.gz",
            "chemistry": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": 1,
            "read1": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L002_R1_001.fastq.gz",
            "read2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L002_R3_001.fastq.gz",
            "read_group": "pbmc_granulocyte_sorted_10k:MissingLibrary:1:HJ2W5DSXY:2",
            "reads_interleaved": false,
            "sample_index": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L002_I1_001.fastq.gz",
            "subsample_rate": 1,
        },
        {
            "barcode": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L003_R2_001.fastq.gz",
            "chemistry": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": 1,
            "read1": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L003_R1_001.fastq.gz",
            "read2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L003_R3_001.fastq.gz",
            "read_group": "pbmc_granulocyte_sorted_10k:MissingLibrary:1:HJ2W5DSXY:3",
            "reads_interleaved": false,
            "sample_index": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L003_I1_001.fastq.gz",
            "subsample_rate": 1,
        },
        {
            "barcode": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L004_R2_001.fastq.gz",
            "chemistry": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": 1,
            "read1": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L004_R1_001.fastq.gz",
            "read2": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L004_R3_001.fastq.gz",
            "read_group": "pbmc_granulocyte_sorted_10k:MissingLibrary:1:HJ2W5DSXY:4",
            "reads_interleaved": false,
            "sample_index": "/net/bmc-lab5/data/kellis/users/benjames/seq/pbmc_granulocyte_sorted_10k/atac/pbmc_granulocyte_sorted_10k_S16_L004_I1_001.fastq.gz",
            "subsample_rate": 1,
        },
    ],
    barcode_whitelist_path = "/net/bmc-lab5/data/kellis/users/benjames/cellranger-arc-2.0.2/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
)
