@include "rna/_basic_sc_rna_counter_stages.mro"

call FILTER_BARCODES(
    sample_id              = "Nodule_3_gex_only",
    matrices_h5            = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/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/chnk0-u3958a38e2d/files/raw_feature_bc_matrix.h5",
    barcode_correction_csv = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/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-u3958a38c90/files/barcode_summary.csv",
    is_antibody_only       = false,
    reference_path         = "/data/adf/meeting_prep/soy_Williams82_v3_with_organelles",
    gem_groups             = [1],
    chemistry_description  = "Single Cell Multiome ATAC + Gene Expression v1",
    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,
        },
        override_library_types:               null,
        override_mode:                        null,
        recovered_cells: {
            per_gem_well: null,
            per_sample:   null,
        },
    },
    target_set             = null,
    chemistry_def          = {
        barcode: [
            {
                kind:      "gel_bead",
                length:    16,
                offset:    0,
                read_type: "R1",
                whitelist: {
                    "name": "737K-arc-v1",
                },
            },
        ],
        description:  "Single Cell Multiome ATAC + Gene Expression v1",
        endedness:    "three_prime",
        name:         "ARC-v1",
        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,
            },
        ],
    },
    multi_graph            = null,
    per_barcode_metrics    = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/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-u3958a38e2d/files/per_barcode_metrics.csv",
    is_spatial             = false,
)
