@include "_sc_rna_counter_stages.mro"

call SUMMARIZE_REPORTS(
    summaries = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_BASIC_REPORTS/fork0/join-u48a5c0d928/files/summary.json",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u48a5c0d8fb/files/summary.json",
        null
    ],
    sample_id = "10X_TCPO",
    sample_desc = "",
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    analysis = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u48a5c0d8fb/files/analysis",
    barcode_summary_h5 = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-u48a5c0cbd7/files/barcode_summary.h5",
    filtered_gene_bc_matrices_h5 = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u48a5c0d4d1/files/filtered_matrices_h5.h5",
    filtered_barcodes = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u48a5c0d4d1/files/filtered_barcodes.csv",
    barcode_whitelist = "3M-february-2018",
    gem_groups = [
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1
    ],
    feature_reference = null,
)