@include "_basic_sc_rna_counter_stages.mro"

call REPORT_MOLECULES(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-ubcfb74562b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-ubcfb74562b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-ubcfb74562c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-ubcfb74562d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk44-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk45-ubcfb74562e/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk46-ubcfb74562f/files/alignments.bam"
    ],
    reference_path = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm9/mm9_usethis",
    feature_reference = null,
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
    barcode_whitelist = "3M-february-2018",
    extract_reads_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-ubcfb74374c/files/summary.json",
    attach_bcs_and_umis_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-ubcfb744548/files/summary.json",
    mark_duplicates_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-ubcfb745612/files/summary.json",
    filtered_barcodes = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_default/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ubcfb745fa4/files/filtered_barcodes.csv",
    recovered_cells = 6000,
    force_cells = null,
)