@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": "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/sym_reprep1",
            "sample_indices": ["any"],
            "sample_names": ["Peak_004_2reprep"],
            "subsample_rate": null,
        },
    ],
    reference_path       = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-GCA_001417965_1_Aiptasia_genome_1_1_genomic",
    feature_reference    = null,
    chemistry_specs      = {
        "Gene Expression": "auto",
    },
    allowed_chems        = [
        "auto",
        "custom",
        "threeprime",
        "fiveprime",
        "SC3Pv1",
        "SC3Pv2",
        "SC3Pv3-polyA",
        "SC3Pv3-CS1",
        # no longer supported, but included to allow DETECT_CHEMISTRY to produce a nice error message
        "SC3Pv3LT",
        "SC3Pv3HT-polyA",
        "SC3Pv3HT-CS1",
        "SC3Pv4-polyA",
        "SC3Pv4-CS1",
        "SC5P-PE",
        "SC5P-PE-v3",
        "SC5P-R2",
        "SC5P-R2-v3",
        "SC5PHT",
        "SC-FB",
        "ARC-v1",
    ],
    r1_length            = null,
    r2_length            = null,
    multi_config         = null,
    is_pd                = false,
    custom_chemistry_def = null,
    feature_config       = null,
)
