@include "rna/_sc_multi_defs.mro"

call MAKE_FULL_CONFIG(
    vdj_t_input        = {
        chain_type:               "TR",
        denovo:                   false,
        force_cells:              null,
        inner_enrichment_primers: null,
        physical_library_id:      "VDJT_1",
        r1_length:                null,
        r2_length:                null,
        sample_def: [
            {
                "fastq_id": "dimitri_TCR",
                "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_TCR"],
                "subsample_rate": null,
                "target_set": null,
                "target_set_name": null,
            },
        ],
    },
    vdj_b_input        = {
        chain_type:               "IG",
        denovo:                   false,
        force_cells:              null,
        inner_enrichment_primers: null,
        physical_library_id:      "VDJB_1",
        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,
            },
        ],
    },
    basic_config       = {
        disable_count:       false,
        disable_multi:       false,
        disable_multi_count: false,
        disable_vdj:         false,
    },
    vdj_reference_path = "/scratch/etanis/ST-118/references/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0",
)
