@include "atac/_cr_atac_stages.mro"

call WRITE_ATAC_BAM(
    num_read_pairs          = 457001034,
    deduped_shards          = [
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk00-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk01-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk02-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk03-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk04-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk05-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk06-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk07-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk08-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk09-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk10-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk11-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk12-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk13-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk14-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk15-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk16-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk17-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk18-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk19-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk20-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk21-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk22-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk23-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk24-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk25-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk26-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk27-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk28-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk29-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk30-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk31-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk32-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk33-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk34-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk35-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk36-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk37-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk38-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk39-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk40-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk41-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk42-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk43-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk44-u3b7f6ea07e/files/deduped_chunk.shard",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/chnk45-u3b7f6ea07e/files/deduped_chunk.shard",
    ],
    reference_path          = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    fastq_defs              = [
        {
            "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,
        },
    ],
    max_items_per_footprint = 40556,
)
