@include "rna/_sc_multi_defs.mro"

call MULTI_GEM_WELL_PROCESSOR(
    gem_group                    = 1,
    sample_id                    = "Nodule_2_gex_only",
    multi_config_sha             = null,
    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,
            },
            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:                  "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_2_gex_only/SC_RNA_COUNTER_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-ua092a46d43/files/gene_index.json",
        include_introns:             true,
        initial_reads:               null,
        min_assignment_confidence:   null,
        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:              "/data/adf/meeting_prep/soy_Williams82_v3_with_organelles",
        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,
            },
        ],
        subsample_rate:              null,
        targeting_method:            null,
        trim_polya_min_score:        20,
        trim_tso_min_score:          20,
    },
    count_chem                   = {
        chemistry_def: {
            barcode: [
                {
                    kind:      "gel_bead",
                    length:    16,
                    offset:    0,
                    read_type: "R1",
                    whitelist: {
                        "name": "737K-arc-v1",
                    },
                },
            ],
            description:  "Single Cell Multiome ATAC + Gene Expression v1",
            endedness:    "three_prime",
            name:         "ARC-v1",
            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,
                },
            ],
        },
        chemistry_type:   "ARC-v1",
        is_antibody_only: false,
    },
    libraries_to_translate       = [],
    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,
    antigen_specificity_controls = null,
)
