@include "rna/_cr_lib_stages.mro"

call WRITE_H5_MATRIX(
    gem_well          = 1,
    counts            = [
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk26-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk27-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk28-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk29-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk30-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk31-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk32-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk33-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk34-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk35-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk36-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk37-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk38-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk39-u3b7f6e8851/files/bc_sort.csf",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk40-u3b7f6e8851/files/bc_sort.csf",
    ],
    feature_reference = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u3b7f6e6062/files/feature_reference.frf.bincode",
    chemistry_def     = {
        barcode: [
            {
                kind:      "gel_bead",
                length:    16,
                offset:    0,
                read_type: "R1",
                whitelist: "737K-arc-v1",
            },
        ],
        description:  "Single Cell Multiome ATAC + Gene Expression v1",
        endedness:    "three_prime",
        name:         "ARC-v1",
        rna: {
            length:     null,
            min_length: null,
            offset:     0,
            read_type:  "R2",
        },
        rna2:         null,
        strandedness: "+",
        umi: {
            length:     12,
            min_length: 10,
            offset:     16,
            read_type:  "R1",
        },
    },
    sample_id         = "pbmc_granulocyte_sorted_10k",
    barcode_index     = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u3b7f6e884e/files/barcode_index.bi.bincode",
)
