@include "atac/_cr_atac_stages.mro"

call WRITE_ATAC_BAM(
    num_read_pairs          = 461993231,
    deduped_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/MARK_ATAC_DUPLICATES/fork0/chnk00-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk01-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk02-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk03-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk04-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk05-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk06-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk07-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk08-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk09-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk10-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk11-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk12-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk13-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk14-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk15-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk16-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk17-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk18-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk19-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk20-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk21-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk22-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk23-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk24-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk25-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk26-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk27-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk28-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk29-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk30-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk31-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk32-u45960dc73a/files/deduped_chunk.shard",
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        "/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/MARK_ATAC_DUPLICATES/fork0/chnk37-u45960dc73a/files/deduped_chunk.shard",
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        "/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/MARK_ATAC_DUPLICATES/fork0/chnk39-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk40-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk41-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk42-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk43-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk44-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk45-u45960dc73a/files/deduped_chunk.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/MARK_ATAC_DUPLICATES/fork0/chnk46-u45960dc73a/files/deduped_chunk.shard",
    ],
    reference_path          = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    fastq_defs              = [
        {
            "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,
        },
    ],
    max_items_per_footprint = 3056,
)
