@include "rna/_sc_multi_defs.mro"

call MULTI_GEM_WELL_PROCESSOR(
    gem_group         = 1,
    common_input      = {
        multi_config_sha: null,
        sample_desc:      "Aiptasia-sym_reprep1",
        sample_id:        "cellranger-Aiptasia-sym_reprep1",
    },
    config            = {
        disable_count:       false,
        disable_multi:       true,
        disable_multi_count: true,
        disable_vdj_b:       true,
        disable_vdj_t:       true,
        disable_vdj_t_gd:    true,
        has_no_vdj_ref:      true,
    },
    is_pd             = false,
    count_inputs      = {
        aligner:                     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,
        custom_chemistry_def:        null,
        feature_reference:           null,
        filter_probes:               null,
        force_sample_barcodes: {
            cells_per_tag:        null,
            non_singlet_barcodes: null,
            sample_barcodes:      null,
        },
        gene_index:                  "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-u29f8cf672c/files/gene_index.json",
        include_exons:               true,
        include_introns:             true,
        initial_reads:               null,
        min_assignment_confidence:   null,
        min_crispr_umi_threshold:    3,
        no_bam:                      false,
        no_target_umi_filter:        false,
        primers: [
            {
                "name": "P5",
                "seq": "AATGATACGGCGACCACCGAGATCT",
            },
            {
                "name": "P7",
                "seq": "CAAGCAGAAGACGGCATACGAGAT",
            },
            {
                "name": "R1",
                "seq": "ACACTCTTTCCCTACACGACG",
            },
            {
                "name": "R2",
                "seq": "GTGACTGGAGTTCAGACGTGTG",
            },
            {
                "name": "switch_oligo",
                "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG",
            },
            {
                "name": "polyA",
                "seq": "AAAAAAAAAAAAAAAAAAAA",
            },
        ],
        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,
            },
        ],
        subsample_rate:              null,
        target_set:                  null,
        target_set_name:             null,
        targeting_method:            null,
        trim_polya_min_score:        20,
        trim_tso_min_score:          20,
    },
    count_chem        = {
        chemistry_defs: {
            Gene Expression: {
                "barcode": [
                    {
                        "kind": "gel_bead",
                        "length": 16,
                        "offset": 0,
                        "read_type": "R1",
                        "whitelist": {
                            "name": "3M-february-2018_TRU",
                            "part": null,
                            "slide": null,
                            "translation": false,
                            "translation_whitelist_path": null,
                        },
                    },
                ],
                "barcode_extraction": null,
                "description": "Single Cell 3' v3 (polyA)",
                "endedness": "three_prime",
                "name": "SC3Pv3-polyA",
                "rna": {
                    "length": null,
                    "min_length": null,
                    "offset": 0,
                    "read_type": "R2",
                },
                "rna2": null,
                "strandedness": "+",
                "umi": [
                    {
                        "length": 12,
                        "min_length": 10,
                        "offset": 16,
                        "read_type": "R1",
                        "whitelist": null,
                    },
                ],
            },
        },
        detected_probe_barcode_pairing: null,
        is_antibody_only:               false,
        probe_barcode_overlap:          null,
    },
    multi_graph       = null,
    vdj_t_inputs      = null,
    vdj_t_chem_def    = null,
    vdj_t_receptor    = null,
    vdj_t_gd_inputs   = null,
    vdj_t_gd_chem_def = null,
    vdj_t_gd_receptor = null,
    vdj_b_inputs      = null,
    vdj_b_chem_def    = null,
    vdj_b_receptor    = null,
    vdj_gen_inputs    = null,
    feature_config    = null,
)
