@include "_basic_sc_rna_counter_stages.mro"

call MARK_DUPLICATES(
    input = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow3/Chow_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SORT_BY_BC/fork0/join-ue9a9a735c1/files/default.bam",
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    filter_umis = true,
    library_info = [
        {
            "gem_group": 1,
            "library_id": "0",
            "library_type": "Gene Expression"
        }
    ],
)