@include "rna/_sc_rna_counter_stages.mro"

call SUMMARIZE_REPORTS as GEX_SUMMARIZE_REPORTS(
    summaries                    = ["/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_CELLS_REPORTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u45960dee69/files/summary.json"],
    sample_id                    = "count-NYU070",
    sample_desc                  = "count-NYU070",
    reference_path               = "/gpfs/data/sequence/cellranger-refdata/refdata-cellranger-arc-GRCh38-2020-A",
    analysis                     = null,
    barcode_summary_h5           = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_GEX_MATRIX_COMPUTER/WRITE_BARCODE_SUMMARY/fork0/chnk0-u45960dd236/files/barcode_summary.h5",
    filtered_gene_bc_matrices_h5 = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/MERGE_ATAC_RNA_MATRICES/fork0/join-u45960deb66/files/gex.h5",
    filtered_barcodes            = "/gpfs/data/sequence/results/aifantislab/2021-runs/2021-07-27/cellranger/count-NYU070/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_JOINT_CELL_DETECTOR/DETECT_JOINT_CELL_BARCODES/fork0/join-u45960dea76/files/cell_barcodes.csv",
    barcode_whitelist            = "737K-arc-v1",
    gem_groups                   = [1],
    feature_reference            = null,
    target_set_name              = null,
    per_feature_metrics_csv      = null,
    include_introns              = true,
)
