fastqc.pbs

#!/bin/bash
#PBS -l nodes=1:ppn=1,walltime=1:00:00
#PBS -N fastqc
#PBS -M ${USER}@nyu.edu
#PBS -m abe
#PBS -o localhost:/scratch/$USER/${PBS_JOBNAME}.o${PBS_JOBID}
#PBS -e localhost:/scratch/$USER/${PBS_JOBNAME}.o${PBS_JOBID}

cd /scratch/$USER

TAG1=$arg1 # this will be the location of the original fastq files

cd ${TAG1}

module load fastqc/0.11.5

gzip -d *.fastq

shopt -s nullglob # Avoid expanding to *.fastq if there were no .fastq files in directory

for f in *.fastq
do
fastqc $f
done

gzip *.fastq

exit 0;