@include "rna/_sc_multi_defs.mro"

call COUNT_ANALYZER(
    filtered_matrices_h5  = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_matrices_h5.h5",
    molecule_info         = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ucc6a7a7ccd/files/molecule_info_non_multiplexed.h5",
    count_inputs          = {
        aligner:                     null,
        cell_calling_config: {
            cell_barcodes:                  null,
            disable_ab_aggregate_detection: false,
            force_cells:                    null,
            override_library_types:         null,
            override_mode:                  null,
            recovered_cells:                null,
        },
        custom_chemistry_def:        null,
        enforce_library_concordance: true,
        feature_reference:           null,
        force_sample_barcodes:       null,
        gene_index:                  "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/FULL_COUNT_INPUTS/WRITE_GENE_INDEX/fork0/chnk0-ucc6a7a71a3/files/gene_index.json",
        include_introns:             false,
        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:              "/scratch/etanis/ST-118/references/refdata-gex-GRCh38-2020-A",
        sample_def: [
            {
                fastq_id:        "dimitri_RNA",
                fastq_mode:      "ILMN_BCL2FASTQ",
                gem_group:       1,
                lanes:           null,
                library_type:    "Gene Expression",
                read_path:       "/scratch/etanis/ST-118/FASTQ/",
                sample_indices:  null,
                sample_names:    ["dimitri_RNA"],
                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,
    },
    no_secondary_analysis = false,
    disable_rna           = true,
    disable_crispr        = true,
    disable_antibody      = true,
    disable_targeted      = true,
    filtered_feature_counts_matrix = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_matrices_h5.h5",
    filtered_barcodes     = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/filtered_barcodes.csv",
    aggregate_barcodes    = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/aggregate_barcodes.csv",
    feature_reference     = null,
    counter_metrics_json  = "/scratch/etanis/ST-118/multi/dimitri-multi/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-ucc6a7a7d61/files/summary.json",
    parse_target_features = {
        bait_fasta:                null,
        disable_target_umi_filter: true,
        disable_targeted:          true,
        probe_set:                 null,
        rps_limit:                 null,
        summary:                   null,
        target_gene_indices:       null,
        target_panel:              null,
        target_panel_or_probe_set: null,
        target_set_name:           null,
        targeting_method:          null,
    },
)
