@include "rna/_basic_sc_rna_counter_stages.mro"

call SUMMARIZE_BASIC_REPORTS(
    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/_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-ucc6a7a7c4d/files/raw_feature_bc_matrix.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",
    per_barcode_metrics     = "/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/_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-ucc6a7a7c4d/files/per_barcode_metrics.csv",
    matrix_computer_summary = "/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/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ucc6a7a7c50/files/summary.json",
    barcode_summary         = "/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/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-ucc6a7a7c4d/files/barcode_summary.h5",
    recovered_cells         = null,
    reference_path          = "/scratch/etanis/ST-118/references/refdata-gex-GRCh38-2020-A",
    summary_jsons           = [
        "/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/_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-ucc6a7a7c50/files/summary.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/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-ucc6a7a7cd4/files/summary.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/_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-ucc6a7a7ccd/files/non_multiplexed_summary.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/FILTER_BARCODES/fork0/join-ucc6a7a7c51/files/summary.json",
    ],
    cell_bcs_only           = false,
)
