@include "_basic_sc_rna_counter_stages.mro"

call REPORT_MOLECULES(
    inputs = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u8c0aa71e99/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u8c0aa71e99/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u8c0aa71e99/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u8c0aa71e9a/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u8c0aa71e9b/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u8c0aa71e9c/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk40-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk41-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk42-u8c0aa71e9d/files/alignments.bam",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk43-u8c0aa71e9d/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/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u8c0aa70d24/files/summary.json",
    attach_bcs_and_umis_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-u8c0aa715b4/files/summary.json",
    mark_duplicates_summary = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-u8c0aa71e80/files/summary.json",
    filtered_barcodes = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u8c0aa725c9/files/filtered_barcodes.csv",
    recovered_cells = null,
    force_cells = null,
)