@include "_basic_sc_rna_counter_stages.mro"

call REPORT_MOLECULES(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u68b572fde8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u68b572fde8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u68b572fde8/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u68b572fde9/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u68b572fdea/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk44-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk45-u68b572fdeb/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk46-u68b572fdec/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk47-u68b572fdec/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk48-u68b572fdec/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk49-u68b572fdec/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk50-u68b572fdec/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk51-u68b572fdec/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk52-u68b572fdec/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk53-u68b572fdec/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_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u68b572d93e/files/summary.json",
    attach_bcs_and_umis_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-u68b572eb05/files/summary.json",
    mark_duplicates_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-u68b572fdc9/files/summary.json",
    filtered_barcodes = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u68b573097e/files/filtered_barcodes.csv",
    recovered_cells = null,
    force_cells = 6000,
)