# Seq Data Folder run=/path/to/seq/data sbatch -p short --job-name bcl2fastq --mem 8000 -t 6:00:00 -o bcl2fq.o -e bcl2fq.o \ --wrap """ module load bcl2fastq/2.20.0.422; cd $run; bcl2fastq \ --use-bases-mask y*,y*,y*,y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0 """