@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-ubebf71cc36/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-ubebf71cc36/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-ubebf71cc36/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-ubebf71cc36/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-ubebf71cc36/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-ubebf71cc36/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-ubebf71cc37/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-ubebf71cc38/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-ubebf71cc39/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-ubebf71cc3a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-ubebf71cc3a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-ubebf71cc3a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-ubebf71cc3b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-ubebf71cc3b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-ubebf71cc3b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-ubebf71cc3b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk45-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk46-ubebf71cc3c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk47-ubebf71cc3d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk48-ubebf71cc3d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk49-ubebf71cc3d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk50-ubebf71cc3d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_G171B_UseThis/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk51-ubebf71cc3d/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_UseThis:0:1:H3LTJBBXX:7",
        "10X_G171B_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",
        "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/updated-usethis-mm10plus-pcg-ercc-lnc-nodups-mcherry",
    threads = 4,
    max_hits_per_read = -1,
)