@include "rna/_sc_multi_defs.mro"

call MULTI_CHEMISTRY_DETECTOR(
    count_inputs        = {
        check_library_compatibility: true,
        chemistry_specs: {
            Gene Expression: "auto",
        },
        custom_chemistry_def:        null,
        feature_reference:           null,
        r1_length:                   null,
        r2_length:                   null,
        reference_path:              "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-GCA_001417965_1_Aiptasia_genome_1_1_genomic",
        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,
            },
        ],
    },
    vdj_inputs          = [],
    vdj_gen_inputs      = null,
    basic_config        = {
        disable_annotate:    true,
        disable_count:       false,
        disable_multi:       true,
        disable_multi_count: true,
        disable_rtl:         true,
        disable_vdj:         true,
    },
    count_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",
    ],
    multi_config        = null,
    is_multi            = false,
    is_pd               = false,
    feature_config      = null,
    vdj_allowed_chems   = null,
)
