@include "_sc_rna_counter_stages.mro"

call SUMMARIZE_REPORTS(
    summaries = [
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_BASIC_REPORTS/fork0/join-udfa19493b2/files/summary.json",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udfa19490af/files/summary.json",
        null
    ],
    sample_id = "tdtomato_run2",
    sample_desc = "",
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    analysis = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-udfa19490af/files/analysis",
    barcode_summary_h5 = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-udfa19442f4/files/barcode_summary.h5",
    filtered_gene_bc_matrices_h5 = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-udfa1947879/files/filtered_matrices_h5.h5",
    filtered_barcodes = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-udfa1947879/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
    ],
    feature_reference = null,
)