@include "rna/sc_multi_core.mro"

call SC_MULTI_CORE(
    common_input          = {
        multi_config_sha: null,
        sample_desc:      "Aiptasia-sym_reprep1",
        sample_id:        "cellranger-Aiptasia-sym_reprep1",
    },
    count_input           = {
        aligner:                     null,
        annotations:                 null,
        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",
        },
        custom_chemistry_def:        null,
        enable_tsne:                 true,
        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",
        genetic_demux_params:        null,
        include_exons:               true,
        include_introns:             true,
        initial_reads:               null,
        min_assignment_confidence:   null,
        min_crispr_umi_threshold:    3,
        no_bam:                      false,
        no_secondary_analysis:       false,
        no_target_umi_filter:        false,
        primer_initial_reads:        null,
        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,
            },
        ],
        skip_cell_annotation:        true,
        special_genomic_regions:     null,
        subsample_rate:              null,
        target_set:                  null,
        target_set_name:             null,
        targeting_method:            null,
        tenx_cloud_token_path:       null,
        tenx_cmos:                   null,
        throughput:                  null,
        trim_polya_min_score:        20,
        trim_tso_min_score:          20,
    },
    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,
    },
    multi_config          = null,
    is_pd                 = false,
    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",
    ],
    vdj_allowed_chems     = null,
    count_pipestance_type = "SC_RNA_COUNTER_CS",
    is_multi              = false,
    feature_config        = null,
    no_preflight          = false,
)
