#!/bin/bash
#PBS -l walltime=01:30:00
#PBS -l nodes=1:ppn=8
#PBS -l vmem=2000mb

# pass in the file name through qsub
echo $f

cd $PBS_O_WORKDIR

module load fastqc/0.10.1
#bedtools should already be in the path

FQ=${f%.bam}
FQ=${FQ##*/}

bedtools bamtofastq -i $f -fq $FQ
fastqc $FQ --outdir .
rm $FQ