@include "rna/_sc_multi_defs.mro"

map call VDJ_CHEMISTRY_DETECTOR(
    vdj_reference_path       = "/scratch/etanis/ST-118/references/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0",
    vdj_chem_inputs          = split split [
        [
            {
                chain_type:           "IG",
                chemistry:            "SCVDJ_auto",
                custom_chemistry_def: 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,
                    },
                ],
            },
            {
                chain_type:           "TR",
                chemistry:            "SCVDJ_auto",
                custom_chemistry_def: null,
                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,
                    },
                ],
            },
        ],
    ],
    gex_chemistry_name       = split ["SC5P-R2"],
    gex_sample_def           = split [
        [
            {
                "fastq_id": "dimitri_RNA",
                "fastq_mode": "ILMN_BCL2FASTQ",
                "gem_group": 1,
                "lanes": null,
                "library_type": "Gene Expression",
                "read_path": "/scratch/etanis/ST-118/FASTQ/",
                "sample_indices": null,
                "sample_names": ["dimitri_RNA"],
                "subsample_rate": null,
                "target_set": null,
                "target_set_name": null,
            },
        ],
    ],
    gex_custom_chemistry_def = split [null],
    disable_count            = false,
)
