Bowtie Template

Executable = /proj/genome/programs/bowtie-0.12.1/bowtie
Arguments = /proj/genome/programs/bowtie-0.12.1/indexes/hg19sp75spike -v 2 -k 11 -m 10 --best --strata -p 4 -q /full/path/to/fastq_file/1184_1_1.fastq --un /full/path/to/unmapped_file/1184_1_1.unmapped.fa --max /full/path/to/repeats_file/1185_1_1.repeat.fa /full/path/to/output_file/1184_1_1.bowtie.txt

Log = bowtie-submit.log.$(Process)
Output = bowtie-submit.out.$(Process)
Error = bowtie-submit.err.$(Process)

request_cpus = 4
request_memory = 8000
request_disk = 0

Queue