@include "_basic_sc_rna_counter_stages.mro"

call REPORT_MOLECULES(
    inputs = [
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk00-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk01-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk02-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk03-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk04-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk05-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk06-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk07-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk08-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk09-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk10-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk11-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk12-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk13-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk14-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk15-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk16-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk17-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk18-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk19-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk20-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk21-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk22-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk23-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk24-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk25-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk26-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk27-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk28-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk29-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk30-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk31-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk32-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk33-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk34-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk35-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk36-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk37-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk38-u85e8944f67/files/alignments.bam",
        "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/chnk39-u85e8944f67/files/alignments.bam"
    ],
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    feature_reference = null,
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
    barcode_whitelist = "3M-february-2018",
    extract_reads_summary = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/SUMMARIZE_READ_REPORTS/fork0/join-u85e893ac5a/files/summary.json",
    attach_bcs_and_umis_summary = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/ATTACH_BCS_AND_UMIS/fork0/join-u85e893ef24/files/summary.json",
    mark_duplicates_summary = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/MARK_DUPLICATES/fork0/join-u85e8944f33/files/summary.json",
    filtered_barcodes = "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u85e8948a9f/files/filtered_barcodes.csv",
    recovered_cells = 10000,
    force_cells = null,
)