@include "_basic_sc_rna_counter_stages.mro"

call REPORT_MOLECULES(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-ud74eb27f4a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-ud74eb27f4a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-ud74eb27f4b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-ud74eb27f4c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-ud74eb27f4d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-ud74eb27f4d/files/alignments.bam"
    ],
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    feature_reference = null,
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
    barcode_whitelist = "737K-august-2016",
    extract_reads_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-ud74eb2730e/files/summary.json",
    attach_bcs_and_umis_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-ud74eb27825/files/summary.json",
    mark_duplicates_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-ud74eb27f35/files/summary.json",
    filtered_barcodes = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-ud74eb28435/files/filtered_barcodes.csv",
    recovered_cells = null,
    force_cells = null,
)