@include "rna/sc_multi_cs.mro"

call FULL_COUNT_INPUTS(
    cs_inputs     = {
        cell_annotation_model:       null,
        cell_calling_config: {
            cell_barcodes:                        null,
            disable_ab_aggregate_detection:       false,
            disable_high_occupancy_gem_detection: false,
            emptydrops_minimum_umis: {
                per_gem_well: null,
                per_sample:   null,
            },
            force_cells: {
                per_gem_well: null,
                per_sample:   null,
            },
            global_minimum_umis: {
                per_gem_well: null,
                per_sample:   null,
            },
            max_mito_percent: {
                per_gem_well: null,
                per_sample:   null,
            },
            override_library_types:               null,
            override_mode:                        null,
            recovered_cells: {
                per_gem_well: null,
                per_sample:   null,
            },
        },
        check_library_compatibility: true,
        chemistry_specs: {
            Gene Expression: "auto",
        },
        feature_reference:           null,
        filter_probes:               null,
        force_sample_barcodes: {
            cells_per_tag:        null,
            non_singlet_barcodes: null,
            sample_barcodes:      null,
        },
        include_introns:             true,
        min_assignment_confidence:   null,
        min_crispr_umi_threshold:    3,
        no_bam:                      false,
        no_secondary_analysis:       false,
        no_target_umi_filter:        false,
        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,
            },
        ],
        skip_cell_annotation:        true,
        target_set:                  null,
        target_set_name:             null,
        targeting_method:            null,
        tenx_cloud_token_path:       null,
        tenx_cmos:                   null,
    },
    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",
    ],
)
