@include "_basic_sc_rna_counter_stages.mro"

call REPORT_MOLECULES(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u0fe2a74895/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u0fe2a74895/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u0fe2a74896/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u0fe2a74897/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u0fe2a74898/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-u0fe2a74899/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk44-u0fe2a7489a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk45-u0fe2a7489a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk46-u0fe2a7489a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk47-u0fe2a7489a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk48-u0fe2a7489a/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/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u0fe2a73613/files/summary.json",
    attach_bcs_and_umis_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-u0fe2a73f9e/files/summary.json",
    mark_duplicates_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-u0fe2a74878/files/summary.json",
    filtered_barcodes = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH2/Nash_2_run/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u0fe2a74ed7/files/filtered_barcodes.csv",
    recovered_cells = null,
    force_cells = null,
)