@include "atac/_atac_matrix_computer.mro"

call _ATAC_MATRIX_COMPUTER(
    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",
    reference_path         = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    assay                  = "arc",
    custom_peaks           = null,
    peak_qval              = null,
    no_bam                 = false,
    sample_id              = "pbmc_granulocyte_sorted_10k",
    sample_desc            = "pbmc_granulocyte_sorted_10k",
)
