@include "_basic_sc_rna_counter_stages.mro"

call MARK_DUPLICATES(
    input = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SORT_BY_BC/fork0/join-udddc741468/files/default.bam",
    reference_path = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm9/mm9_usethis",
    filter_umis = true,
    library_info = [
        {
            "gem_group": 1,
            "library_id": "0",
            "library_type": "Gene Expression"
        }
    ],
)