@include "rna/_basic_sc_rna_counter_stages.mro"

call FILTER_BARCODES(
    sample_id              = "dimitri_RNA_only",
    matrices_h5            = "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed616/files/raw_feature_bc_matrix.h5",
    barcode_correction_csv = "/scratch/etanis/software/cellranger-6.1.2/dimitri_RNA_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-ufc475ed154/files/barcode_summary.csv",
    is_antibody_only       = false,
    reference_path         = "/scratch/etanis/refs/10x_ref/refdata-gex-GRCh38-2020-A",
    gem_groups             = [1],
    chemistry_description  = "Single Cell 5' R2-only",
    config                 = {
        cell_barcodes:                  null,
        disable_ab_aggregate_detection: false,
        force_cells:                    null,
        override_library_types:         null,
        override_mode:                  null,
        recovered_cells:                null,
    },
)
