@include "atac/_sc_atac_analyzer_stages.mro"

call PERFORM_DIFFERENTIAL_ANALYSIS as COMPUTE_DIFFERENTIAL_ATAC(
    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",
    filtered_peak_bc_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_tf_bc_matrix   = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/GENERATE_TF_MATRIX/fork0/join-u3b7f6eb902/files/filtered_tf_bc_matrix.h5",
    factorization           = ["lsa"],
    clustering              = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_ATAC_CLUSTERING_COMPUTER/COMBINE_CLUSTERING/fork0/chnk0-u3b7f6eb946/files/clustering",
)
