@include "_basic_sc_rna_counter_stages.mro"

call SUMMARIZE_BASIC_REPORTS(
    extract_reads_summary = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-udfa193a13b/files/summary.json",
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
    attach_bcs_and_umis_summary = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-udfa193d804/files/summary.json",
    mark_duplicates_summary = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-udfa19437e1/files/summary.json",
    count_genes_reporter_summary = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-udfa19442f4/files/reporter_summary.json",
    filter_barcodes_summary = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-udfa1947879/files/summary.json",
    subsample_molecules_summary = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUBSAMPLE_READS/fork0/join-udfa1948c4d/files/summary.json",
    raw_gene_bc_matrices_h5 = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-udfa19442f4/files/matrices_h5.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",
    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
    ],
)