@include "rna/_sc_multi_defs.mro"

call COUNT_ANALYZER(
    filtered_matrices_h5  = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/filtered_matrices_h5.h5",
    molecule_info         = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/join-u29f8cfd3d5/files/molecule_info_non_multiplexed.h5",
    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,
    },
    no_secondary_analysis = false,
    disable_rna           = false,
    disable_crispr        = true,
    disable_antibody      = true,
    disable_antigen       = true,
    is_pd                 = false,
    disable_targeted      = true,
    enable_tsne           = true,
    filtered_barcodes     = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u29f8cfca16/files/filtered_barcodes.csv",
    aggregate_barcodes    = null,
    feature_reference     = null,
    multi_graph           = null,
    counter_metrics_json  = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-Aiptasia-sym_reprep1/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u29f8cfd517/files/summary.json",
    parse_target_features = {
        bait_fasta:                null,
        disable_target_umi_filter: true,
        disable_targeted:          true,
        no_bam:                    false,
        probe_set:                 null,
        target_gene_indices:       null,
        target_panel:              null,
        target_panel_or_probe_set: null,
        target_panel_summary:      null,
        target_set_name:           null,
        targeting_method:          null,
    },
    sample_id             = null,
)
