@include "atac_rna/_joint_cell_detector_stages.mro"

call DETECT_JOINT_CELL_BARCODES(
    reference_path    = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    barcode_whitelist = "737K-arc-v1",
    rna_raw_matrix    = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_H5_MATRIX/fork0/chnk0-u45960dd236/files/raw_feature_bc_matrix.h5",
    atac_raw_matrix   = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/GENERATE_PEAK_MATRIX/fork0/join-u45960ddf9a/files/raw_matrix.h5",
    force_cells       = null,
    atac_excluded_bcs = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_EXCLUDED_BARCODES/fork0/chnk0-u45960de7df/files/excluded_barcodes.json",
)
