@include "rna/_sc_multi_defs.mro"

call VDJ_GEM_WELL_PROCESSOR as VDJ_B_GEM_WELL_PROCESSOR(
    sample_id             = "dimitri-multi",
    chemistry_type        = "SCVDJ-R2",
    receptor              = "IG",
    inputs                = {
        custom_chemistry_def:     null,
        denovo:                   false,
        force_cells:              null,
        initial_reads:            null,
        inner_enrichment_primers: null,
        r1_length:                null,
        r2_length:                null,
        sample_def: [
            {
                "fastq_id": "dimitri_BCR",
                "fastq_mode": "ILMN_BCL2FASTQ",
                "gem_group": 1,
                "lanes": null,
                "library_type": "VDJ",
                "read_path": "/scratch/etanis/ST-118/FASTQ/",
                "sample_indices": null,
                "sample_names": ["dimitri_BCR"],
                "subsample_rate": null,
                "target_set": null,
                "target_set_name": null,
            },
        ],
        subsample_rate:           null,
    },
    gen_inputs            = {
        reference_path:     "/scratch/etanis/ST-118/references/refdata-gex-GRCh38-2020-A",
        vdj_reference_path: "/scratch/etanis/ST-118/references/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0",
    },
    gex_filtered_barcodes = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_barcodes.csv",
    is_antibody_only      = false,
    is_non_targeted_gex   = true,
)
