@include "rna/_cr_lib_stages.mro"

call WRITE_H5_MATRIX(
    gem_well                  = 1,
    counts                    = [
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk11-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk12-u9474a469ce/files/bc_sort.csf",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk13-u9474a469ce/files/bc_sort.csf",
    ],
    feature_reference         = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/MAKE_SHARD/fork0/split-u9474a46535/files/feature_reference.frf.bincode",
    chemistry_def             = {
        barcode: [
            {
                kind:      "gel_bead",
                length:    16,
                offset:    0,
                read_type: "R1",
                whitelist: {
                    "name": "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",
                whitelist:  null,
            },
        ],
    },
    sample_id                 = "Nodule_1gex_only",
    barcode_index             = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_1gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_INDEX/fork0/chnk0-u9474a469ce/files/barcode_index.bi.bincode",
    slide_serial_capture_area = null,
)
