@include "atac_rna/sc_atac_gex_counter_stages.mro"

call MERGE_RNA_ATAC_DATA(
    disable_atac         = false,
    disable_rna          = false,
    reference_path       = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    atac_whitelist       = "737K-arc-v1",
    rna_whitelist        = "737K-arc-v1",
    rna_summary          = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u3b7f6eb8a8/files/metrics_summary_json.json",
    atac_summary         = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u3b7f6eb7d3/files/summary.json",
    joint_summaries      = [
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_CELL_METRICS/fork0/chnk0-u3b7f6eb4ba/files/merged_summary.json",
        "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_FEATURE_LINKAGE_COMPUTER/COMPUTE_FEATURE_LINKAGES/fork0/join-u3b7f6eb950/files/summary.json",
    ],
    atac_metrics         = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_METRIC_COLLECTOR/MERGE_SINGLECELL_METRICS/fork0/chnk0-u3b7f6eb6ce/files/singlecell.csv",
    rna_metrics          = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/COMPILE_GEX_BARCODE_METRICS/fork0/chnk0-u3b7f6eb4ba/files/augmented_metrics.csv",
    joint_metrics        = "/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/singlecell.csv",
    atac_matrix          = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u3b7f6eafbe/files/raw_matrix.h5",
    rna_matrix           = "/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_atac_matrix = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u3b7f6eb558/files/atac.h5",
    filtered_rna_matrix  = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u3b7f6eb558/files/gex.h5",
    atac_summary_csv_cs  = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_REPORTER/SUMMARIZE_REPORTS_SINGLECELL/fork0/chnk0-u3b7f6eb7d3/files/summary_csv.csv",
    rna_summary_csv_cs   = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/GEX_SUMMARIZE_REPORTS/fork0/chnk0-u3b7f6eb8a8/files/metrics_summary_csv.csv",
)
