@include "atac/_cr_atac_stages.mro"

call ALIGN_ATAC_READS(
    reference_path         = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    shards                 = [
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk0-u3b7f6e6060/files/out.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk1-u3b7f6e6060/files/out.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk2-u3b7f6e6060/files/out.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/chnk3-u3b7f6e6060/files/out.shard",
    ],
    chunk_chemistry_map    = [
        "3p;fwd",
        "3p;fwd",
        "3p;fwd",
        "3p;fwd",
    ],
    barcode_counts         = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MAKE_ATAC_SHARDS/fork0/join-u3b7f6e6040/files/barcode_counts.bch.bincode",
    barcode_whitelist_path = "/net/bmc-lab5/data/kellis/users/benjames/cellranger-arc-2.0.2/lib/python/atac/barcodes/737K-arc-v1.txt.gz",
    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,
        },
    ],
    assay                  = "arc",
    num_read_pairs         = 457001034,
)
