@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-u401229ed99/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-u401229ed99/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-u401229ed99/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-u401229ed99/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-u401229ed99/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-u401229ed9a/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-u401229ed9b/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-u401229ed9c/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-u401229ed9d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk45-u401229ed9d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk46-u401229ed9d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk47-u401229ed9d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk48-u401229ed9d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk49-u401229ed9d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk50-u401229ed9d/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk51-u401229ed9d/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1:H3LTJBBXX:7",
        "10X_G171B_mm10:0:1: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 = "/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/mm10_ref/updated-usethis-mm10plus-pcg-ercc-lnc-nodups",
    threads = 4,
    max_hits_per_read = -1,
)