@include "rna/_cr_lib_stages.mro"

call WRITE_H5_MATRIX(
    gem_well          = 1,
    counts            = [
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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/chnk14-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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/chnk15-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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/chnk16-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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/chnk17-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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/chnk18-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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/chnk19-ufc475ed154/files/bc_sort.csf",
        "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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/chnk20-ufc475ed154/files/bc_sort.csf",
    ],
    feature_reference = "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ecb9b/files/feature_reference.frf.bincode",
    chemistry_def     = {
        barcode: [
            {
                kind:      "gel_bead",
                length:    16,
                offset:    0,
                read_type: "R1",
                whitelist: "737K-august-2016",
            },
        ],
        description:  "Single Cell 5' R2-only",
        endedness:    "five_prime",
        name:         "SC5P-R2",
        rna: {
            length:     null,
            min_length: null,
            offset:     0,
            read_type:  "R2",
        },
        rna2:         null,
        strandedness: "-",
        umi: {
            length:     10,
            min_length: null,
            offset:     16,
            read_type:  "R1",
        },
    },
    sample_id         = "dimitri_RNA_only",
    barcode_index     = "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/barcode_index.bi.bincode",
)
