@include "atac_rna/_joint_cell_detector_stages.mro"

call MERGE_ATAC_RNA_MATRICES(
    sample_id            = "pbmc_granulocyte_sorted_10k",
    atac_raw_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",
    atac_filtered_matrix = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/FILTER_PEAK_MATRIX/fork0/join-u3b7f6eb4ba/files/filtered_matrix.h5",
    rna_raw_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",
    rna_filtered_matrix  = "/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/filtered_matrix.h5",
    barcode_whitelist    = "737K-arc-v1",
    reference_path       = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
)
