@include "_basic_sc_rna_counter_stages.mro"

call SUMMARIZE_BASIC_REPORTS(
    extract_reads_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u9daea75c7b/files/summary.json",
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
    attach_bcs_and_umis_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-u9daea7689b/files/summary.json",
    mark_duplicates_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-u9daea77c3f/files/summary.json",
    count_genes_reporter_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-u9daea77e5a/files/reporter_summary.json",
    filter_barcodes_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u9daea788b6/files/summary.json",
    subsample_molecules_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUBSAMPLE_READS/fork0/join-u9daea78d5c/files/summary.json",
    raw_gene_bc_matrices_h5 = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/join-u9daea77e5a/files/matrices_h5.h5",
    filtered_gene_bc_matrices_h5 = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH3/Nash_3_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u9daea788b6/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,
        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
    ],
)