@include "atac/_peak_caller_stages.mro"

call DETECT_PEAKS(
    sample_id       = "human_brain_3k",
    sample_desc     = "human_brain_3k",
    assay           = "arc",
    cut_sites       = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud1886fa497/files/cut_sites.bedgraph",
    reference_path  = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    count_dict      = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_PEAK_CALLER/COUNT_CUT_SITES/fork0/chnk0-ud1886fa497/files/count_dict.json",
    custom_peaks    = null,
    qval            = null,
    fragments       = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud1886f9d6f/files/fragments.tsv.gz",
    fragments_index = "/home/benjames/data4/10X/human_brain_3k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-ud1886f9d6f/files/fragments.tsv.gz.tbi",
)
