@include "_basic_sc_rna_counter_stages.mro"

call REPORT_MOLECULES(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u6ddfc30b65/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u6ddfc30b66/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u6ddfc30b67/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u6ddfc30b67/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u6ddfc30b67/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u6ddfc30b67/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-u6ddfc30b68/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk44-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk45-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk46-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk47-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk48-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk49-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk50-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk51-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk52-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk53-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk54-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk55-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk56-u6ddfc30b69/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk57-u6ddfc30b69/files/alignments.bam"
    ],
    reference_path = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/mm10_premrna_v1.1_ensembl_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/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u6ddfc2ee11/files/summary.json",
    attach_bcs_and_umis_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-u6ddfc2f846/files/summary.json",
    mark_duplicates_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-u6ddfc30b40/files/summary.json",
    filtered_barcodes = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO_premRNA_Gene/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u6ddfc31616/files/filtered_barcodes.csv",
    recovered_cells = null,
    force_cells = null,
)