@include "atac/_peak_annotator_stages.mro"

call GENERATE_TF_MATRIX(
    reference_path  = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    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",
    peak_motif_hits = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/SCAN_MOTIFS/fork0/join-u3b7f6eb8c7/files/peak_motif_hits.bed",
    filtered_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",
)
