@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-ue6fc72d6a2/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-ue6fc72d6a2/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-ue6fc72d6a2/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-ue6fc72d6a2/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-ue6fc72d6a2/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-ue6fc72d6a2/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-ue6fc72d6a3/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-ue6fc72d6a4/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171C_mm9_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-ue6fc72d6a5/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171C_mm9_UseThis: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"
    ],
    reference_path = "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm9/mm9_usethis",
    threads = 4,
    max_hits_per_read = -1,
)