@include "rna/_basic_sc_rna_counter_stages.mro"

call SUMMARIZE_BASIC_REPORTS(
    matrices_h5             = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u3b7f6ea5a5/files/raw_feature_bc_matrix.h5",
    filtered_barcodes       = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u3b7f6eb4a6/files/cell_barcodes.csv",
    per_barcode_metrics     = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/COLLATE_METRICS/fork0/chnk0-u3b7f6ea5e9/files/per_barcode_metrics.csv",
    matrix_computer_summary = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3b7f6ea89e/files/summary.json",
    barcode_summary         = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u3b7f6ea5a5/files/barcode_summary.h5",
    recovered_cells         = 1000,
    reference_path          = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    summary_jsons           = [
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/MERGE_METRICS/fork0/chnk0-u3b7f6ea89e/files/summary.json",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUBSAMPLE_READS/fork0/join-u3b7f6eb504/files/summary.json",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/WRITE_MOLECULE_INFO/fork0/chnk0-u3b7f6eb4ba/files/non_multiplexed_summary.json",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_UMI_MATRIX/fork0/join-u3b7f6eb4ba/files/summary.json",
    ],
    cell_bcs_only           = false,
)
