@include "rna/_cr_lib_stages.mro"

call WRITE_H5_MATRIX(
    gem_well          = 1,
    counts            = [
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk14-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk15-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk16-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk17-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk18-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk19-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk20-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk21-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk22-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk23-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk24-ud1886f8d28/files/bc_sort.csf",
        "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk25-ud1886f8d28/files/bc_sort.csf",
    ],
    feature_reference = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-ud1886f6d8a/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         = "human_brain_3k",
    barcode_index     = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-ud1886f8d25/files/barcode_index.bi.bincode",
)
