@include "rna/_sc_rna_counter_stages.mro"

call SUMMARIZE_REPORTS(
    summaries                    = [
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/MERGE_METRICS/fork0/chnk0-uac0168ad1f/files/summary.json",
        "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-uac0168ad54/files/summary.json",
        null,
        null,
        null,
    ],
    sample_id                    = "count-PAXUGA_Relapse",
    sample_desc                  = "",
    reference_path               = "/gpfs/data/sequence/cellranger-refdata/refdata-gex-GRCh38-2020-A",
    analysis                     = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/COUNT_ANALYZER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-uac0168ad54/files/analysis",
    barcode_summary_h5           = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/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-uac0168a094/files/barcode_summary.h5",
    filtered_gene_bc_matrices_h5 = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-uac0168a0cc/files/filtered_matrices_h5.h5",
    filtered_barcodes            = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-09-27/cellranger/count-PAXUGA_Relapse/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-uac0168a0cc/files/filtered_barcodes.csv",
    barcode_whitelist            = "3M-february-2018",
    gem_groups                   = [1],
    feature_reference            = null,
    target_set_name              = null,
    per_feature_metrics_csv      = null,
    include_introns              = false,
)
