@include "rna/_sc_rna_counter_stages.mro"

call SUMMARIZE_REPORTS(
    summaries                    = [
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-u3958a39420/files/summary.json",
        "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3958a3935d/files/summary.json",
        null,
        null,
        null,
        null,
    ],
    sample_id                    = "Nodule_3_gex_only",
    sample_desc                  = "",
    reference_path               = "/data/adf/meeting_prep/soy_Williams82_v3_with_organelles",
    analysis                     = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u3958a3935d/files/analysis",
    barcode_summary_h5           = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u3958a38e2d/files/barcode_summary.h5",
    filtered_gene_bc_matrices_h5 = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3958a38e35/files/filtered_matrices_h5.h5",
    filtered_barcodes            = "/data/adf/meeting_prep/glyma.nodule_multiome/Nodule_3_gex_only/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u3958a38e35/files/filtered_barcodes.csv",
    target_panel_summary         = null,
    barcode_whitelist            = "737K-arc-v1",
    antibody_histograms          = null,
    antibody_treemap             = null,
    antigen_histograms           = null,
    antigen_treemap              = null,
    feature_reference            = null,
    target_set_name              = null,
    per_feature_metrics_csv      = null,
    include_introns              = true,
    throughput                   = null,
)
