@include "_common_stages.mro"

call CELLRANGER_PREFLIGHT_LOCAL(
    sample_def = [
        {
            "gem_group": null,
            "lanes": null,
            "sample_names": [
                "H2B-myonuclei"
            ],
            "sample_indices": [
                "any"
            ],
            "fastq_mode": "ILMN_BCL2FASTQ",
            "read_path": "/orange/ewang/lancetdenes/190979853/fastq_files/h2b"
        }
    ],
    chemistry_name = "auto",
    custom_chemistry_def = null,
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    feature_reference = null,
    check_executables = false,
    recovered_cells = 10000,
    force_cells = null,
    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,
)