@include "rna/_basic_sc_rna_counter_stages.mro"

call FILTER_BARCODES(
    sample_id              = "count-PAXUGA_Relapse",
    matrices_h5            = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/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-uac0168a094/files/raw_feature_bc_matrix.h5",
    barcode_correction_csv = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/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-uac01688bf7/files/barcode_summary.csv",
    is_antibody_only       = false,
    reference_path         = "/gpfs/data/sequence/cellranger-refdata/refdata-gex-GRCh38-2020-A",
    gem_groups             = [1],
    chemistry_description  = "Single Cell 3' v3",
    config                 = {
        cell_barcodes:                  null,
        disable_ab_aggregate_detection: false,
        force_cells:                    null,
        override_library_types:         null,
        override_mode:                  null,
        recovered_cells:                null,
    },
)
