@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-u48a5c0ac47/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-u48a5c0ac47/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-u48a5c0ac47/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-u48a5c0ac48/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-u48a5c0ac49/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-u48a5c0ac4a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk45-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk46-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk47-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk48-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk49-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk50-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk51-u48a5c0ac4c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk52-u48a5c0ac4d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk53-u48a5c0ac4d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk54-u48a5c0ac4d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk55-u48a5c0ac4d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk56-u48a5c0ac4d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G172/10X_TCPO/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk57-u48a5c0ac4d/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:1",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:2",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:3",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4",
        "10X_TCPO:0:1:HM3TJBGXC:4"
    ],
    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",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression"
    ],
    reference_path = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    threads = 4,
    max_hits_per_read = -1,
)