@include "rna/_cr_lib_stages.mro"

call BARCODE_CORRECTION(
    gem_well               = 1,
    invalid_uncorrected    = ["/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/chnk0-ucc6a7a71c0/files/invalid.shard"],
    chemistry_def          = {
        barcode: [
            {
                kind:      "gel_bead",
                length:    16,
                offset:    0,
                read_type: "R1",
                whitelist: "737K-august-2016",
            },
        ],
        description:  "Single Cell V(D)J R2-only",
        endedness:    "five_prime",
        name:         "SCVDJ-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",
        },
    },
    barcode_segment_counts = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join-ucc6a7a71c0/files/barcode_segment_counts.bsc.bincode",
    barcode_counts         = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join-ucc6a7a71c0/files/barcode_counts.bcc.bincode",
    valid_read_metrics     = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/VDJ_T_GEM_WELL_PROCESSOR/SC_VDJ_CONTIG_ASSEMBLER/MAKE_SHARD/fork0/join-ucc6a7a71c0/files/bc_correct_summary.bcm.bincode",
    libraries_to_translate = [],
)
