@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-udddc73f45f/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-udddc73f460/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-udddc73f461/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk45-udddc73f462/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk46-udddc73f463/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk47-udddc73f463/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk48-udddc73f463/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk49-udddc73f463/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk50-udddc73f463/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_mm9_2000cells/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk51-udddc73f463/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7",
        "10X_G171B_mm9_2000cells:0:1:H3LTJBBXX:7"
    ],
    library_types = [
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression"
    ],
    reference_path = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm9/mm9_usethis",
    threads = 4,
    max_hits_per_read = -1,
)