@include "rna/_basic_sc_rna_counter_stages.mro"

call FILTER_BARCODES(
    chemistry_defs         = {
        "Gene Expression": {
            barcode: [
                {
                    kind:      "gel_bead",
                    length:    16,
                    offset:    0,
                    read_type: "R1",
                    whitelist: {
                        name:                       "3M-february-2018_TRU",
                        part:                       null,
                        slide:                      null,
                        translation:                false,
                        translation_whitelist_path: null,
                    },
                },
            ],
            barcode_extraction: null,
            description:        "Single Cell 3' v3 (polyA)",
            endedness:          "three_prime",
            name:               "SC3Pv3-polyA",
            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,
                },
            ],
        },
    },
    sample_id              = "cellranger-Aiptasia-sym_reprep1",
    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/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/join-u29f8cfca0b/files/raw_feature_bc_matrix.h5",
    barcode_correction_csv = "/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/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-u29f8cf69be/files/barcode_summary.csv",
    is_antibody_only       = false,
    reference_path         = "/oak/stanford/groups/akundaje/marinovg/various/2025-02-27-Tingting-scRNA-seq/cellranger-GCA_001417965_1_Aiptasia_genome_1_1_genomic",
    gem_groups             = [1],
    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,
        },
    },
    target_set             = null,
    multi_graph            = null,
    per_barcode_metrics    = "/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/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u29f8cfca0d/files/per_barcode_metrics.csv",
    is_spatial             = false,
)
