@include "atac_rna/_joint_cell_detector_stages.mro"

call GENERATE_SC_ATAC_COUNTS(
    fragments         = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u3b7f6ea07b/files/fragments.tsv.gz",
    fragments_index   = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u3b7f6ea07b/files/fragments.tsv.gz.tbi",
    peaks             = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/DETECT_PEAKS/fork0/join-u3b7f6eabbf/files/peaks.bed",
    reference_path    = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    cell_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/atac_formatted_cell_barcodes.csv",
    excluded_barcodes = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u3b7f6eb4a5/files/excluded_barcodes.json",
)
