@include "_chemistry_detector_stages.mro"

call DETECT_CHEMISTRY(
    sample_id = "10X_Chow_2",
    sample_def = [
        {
            "gem_group": null,
            "lanes": null,
            "sample_names": [
                "chow2"
            ],
            "sample_indices": [
                "any"
            ],
            "fastq_mode": "ILMN_BCL2FASTQ",
            "read_path": "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow2/Chow-2_MissingLibrary_1_HKWLTBGX3"
        }
    ],
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    vdj_reference_path = null,
    chemistry_name_spec = "auto",
    allowed_chems = [
        "auto",
        "custom",
        "threeprime",
        "fiveprime",
        "SC3P_auto",
        "SC5P_auto",
        "SC3Pv1",
        "SC3Pv2",
        "SC3Pv3",
        "SC5P-PE",
        "SC5P-R2",
        "SC5P-R1",
        "SC-FB"
    ],
    r1_length = null,
    r2_length = null,
)