@include "rna/_cr_lib_stages.mro"

call DETECT_CHEMISTRY(
    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,
        },
    ],
    reference_path      = null,
    feature_reference   = null,
    chemistry_name_spec = "SCVDJ_auto",
    allowed_chems       = [
        "SCVDJ_auto",
        "custom",
        "SCVDJ",
        "SCVDJ-R2",
        "SCVDJ-R1",
    ],
    r1_length           = null,
    r2_length           = null,
)
