#!/bin/sh
#$ -S /bin/sh

#$ -pe smp 24
#$ -cwd
#$ -V

#### Jobname
#$ -N FASTQC

#### Error Outputfile
#$ -e FASTQC.err
#$ -o FASTQC.log

#### Resubmit
#$ -r y

#working directory
folder="/data/projects/2018/IBD/ATAC_BCG/"

#input files
allfiles=$folder
allfiles+="02_TRIM/*.fastq.gz"

#output folder
outfolder=$folder
outfolder+="01_FASTQC/"

for files in $allfiles;
do
 
fastqc -t 24 -o $outfolder $files

done
