@include "rna/_cr_lib_stages.mro"

call BARCODE_CORRECTION(
    gem_well               = 1,
    invalid_uncorrected    = ["/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_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/chnk0-u3958a388ce/files/invalid.shard"],
    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,
            },
        ],
    },
    barcode_segment_counts = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_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/join-u3958a388cd/files/barcode_segment_counts.bsc.bincode",
    barcode_counts         = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_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/join-u3958a388cd/files/barcode_counts.bcc.bincode",
    valid_read_metrics     = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_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/join-u3958a388cd/files/bc_correct_summary.bcm.bincode",
    libraries_to_translate = [],
    min_reads_to_report_bc = 1000,
)
