@include "rna/_cr_lib_stages.mro"

call DETECT_CHEMISTRY as DETECT_COUNT_CHEMISTRY(
    sample_def                   = [
        {
            "fastq_id": null,
            "fastq_mode": "ILMN_BCL2FASTQ",
            "gem_group": null,
            "lanes": null,
            "library_type": "Gene Expression",
            "read_path": "/data/adf/meeting_prep/glyma.nodule_multiome/fastq/Nodule_2/RNA",
            "sample_indices": ["any"],
            "sample_names": ["Nodule_2"],
            "subsample_rate": null,
            "target_set": null,
            "target_set_name": null,
        },
    ],
    reference_path               = "/data/adf/meeting_prep/soy_Williams82_v3_with_organelles",
    feature_reference            = null,
    chemistry_name_spec          = "ARC-v1",
    allowed_chems                = [
        "auto",
        "custom",
        "threeprime",
        "fiveprime",
        "SC3P_auto",
        "SC5P_auto",
        "SC3Pv1",
        "SC3Pv2",
        "SC3Pv3",
        "SC3Pv3LT",
        "SC3Pv3HT",
        "SC5P-PE",
        "SC5P-R1",
        "SC5P-R2",
        "SC5PHT",
        "SC-FB",
        "ARC-v1",
    ],
    r1_length                    = null,
    r2_length                    = null,
    multi_config                 = null,
    is_pd                        = false,
    custom_chemistry_def         = null,
    antigen_specificity_controls = null,
)
