@include "atac/_atac_cloupe_stages.mro"

call ATAC_CLOUPE_PREPROCESS as ATAC_GEX_CLOUPE_PREPROCESS(
    pipestance_type        = "SC_ATAC_GEX_COUNTER",
    sample_id              = "pbmc_granulocyte_sorted_10k",
    sample_desc            = "pbmc_granulocyte_sorted_10k",
    reference_path         = "/home/Genomes/cellranger/refdata-cellranger-arc-GRCh38-2020-A-2.0.0",
    analysis               = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/analysis_h5.h5",
    feature_barcode_matrix = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/ATAC_GEX_SUMMARIZE_ANALYSIS/fork0/join-u3b7f6ec6d4/files/loupe_matrix_h5.h5",
    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",
    fragments_index        = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/MARK_ATAC_DUPLICATES/fork0/join-u3b7f6ea07b/files/fragments.tsv.gz.tbi",
    metrics_json           = "/home/benjames/data4/10X/pbmc_granulocyte_sorted_10k/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/MERGE_RNA_ATAC_DATA/fork0/join-u3b7f6ec6d4/files/summary.json",
    aggregation_csv        = null,
    gem_group_index_json   = null,
    no_secondary_analysis  = false,
)
