@include "_basic_sc_rna_counter_stages.mro"

call ALIGN_READS(
    reads = [
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-ud74eb27144/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-ud74eb27145/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-ud74eb27146/files/reads.fastq/1.fastq.lz4",
        "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/NASH1/Nash1/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-ud74eb27147/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    read_groups = [
        "Nash1:0:1:HKWLTBGX3:1",
        "Nash1:0:1:HKWLTBGX3:1",
        "Nash1:0:1:HKWLTBGX3:1",
        "Nash1:0:1:HKWLTBGX3:1",
        "Nash1:0:1:HKWLTBGX3:1",
        "Nash1:0:1:HKWLTBGX3:1",
        "Nash1:0:1:HKWLTBGX3:1",
        "Nash1:0:1:HKWLTBGX3:2",
        "Nash1:0:1:HKWLTBGX3:2",
        "Nash1:0:1:HKWLTBGX3:2",
        "Nash1:0:1:HKWLTBGX3:2",
        "Nash1:0:1:HKWLTBGX3:2",
        "Nash1:0:1:HKWLTBGX3:2",
        "Nash1:0:1:HKWLTBGX3:2",
        "Nash1:0:1:HKWLTBGX3:3",
        "Nash1:0:1:HKWLTBGX3:3",
        "Nash1:0:1:HKWLTBGX3:3",
        "Nash1:0:1:HKWLTBGX3:3",
        "Nash1:0:1:HKWLTBGX3:3",
        "Nash1:0:1:HKWLTBGX3:3",
        "Nash1:0:1:HKWLTBGX3:3",
        "Nash1:0:1:HKWLTBGX3:4",
        "Nash1:0:1:HKWLTBGX3:4",
        "Nash1:0:1:HKWLTBGX3:4",
        "Nash1:0:1:HKWLTBGX3:4",
        "Nash1:0:1:HKWLTBGX3:4",
        "Nash1:0:1:HKWLTBGX3:4",
        "Nash1:0:1:HKWLTBGX3:4"
    ],
    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"
    ],
    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,
)