@include "rna/sc_rna_counter_cs.mro"

call _STRUCTIFY(
    common_input = {
        multi_config_sha: null,
        sample_desc:      "Aiptasia-sym_reprep1",
        sample_id:        "cellranger-Aiptasia-sym_reprep1",
    },
    count_input  = {
        aligner:                     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",
        },
        emptydrops_minimum_umis:     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/WRITE_GENE_INDEX/fork0/chnk0-u29f8cf672c/files/gene_index.json",
        global_minimum_umis:         null,
        include_introns:             true,
        max_mito_percent:            null,
        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,
        trim_polya_min_score:        20,
        trim_tso_min_score:          20,
    },
)
