Wrapper script for paired-end cutadapt

cutadapt_em_PE.sh

#!/bin/bash

cutadapt=`which cutadapt`
fastqc=`which fastqc`
origdir=".."
results="."
fastqcdir="${results}/FastQC"
adapter5="CTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
adapter3="GATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
inprefix="C"
outprefix="D"
samples=2
replicates=3

if ! [ -d "$results" ];
then
        mkdir -p $results
fi

if ! [ -d "$fastqcdir" ];
then
        mkdir -p $fastqcdir
fi

for s in $(seq 1 $samples)
do
        for r in $(seq 1 $replicates)
        do
        sample=${inprefix}${s}_R${r}
        outsample=${outprefix}${s}_R${r}
        echo "processing $sample"
        rd1="${origdir}/${sample}_1.fastq"
        rd2="${origdir}/${sample}_2.fastq"
        outrd1="${results}/${outsample}_1.fastq"
        outrd2="${results}/${outsample}_2.fastq"
        echo "infiles $rd1 && $rd2"
        echo "outfiles $outrd1 && $outrd2"
        if ! [ -f "$rd1" ];
        then
                echo "ERROR: $rd1 not available"
        fi
        if ! [ -f "$rd2" ];
        then
                echo "ERROR: $rd2 not available"
        fi
        set -x
        # run cutadapt in paired-end mode
        $cutadapt -q 30 -m 25 -g $adapter5 -a $adapter3 --paired-output tmp.2.fastq -o tmp.1.fastq $rd1 $rd2 1> cutadapt_${sample}.run1.out 2> cutadapt_${sample}.run1.err
        $cutadapt -q 30 -m 25 -g $adapter5 -a $adapter3 --paired-output $outrd1 -o $outrd2 tmp.2.fastq tmp.1.fastq 1> cutadapt_${sample}.run2.out 2> cutadapt_${sample}.run2.err
        # remove temp files
        rm tmp.1.fastq tmp.2.fastq
        # run FastQC
        $fastqc --quiet --noextract -o $fastqcdir -t 16 $outrd1
        $fastqc --quiet --noextract -o $fastqcdir -t 16 $outrd2
        # gzip output
        gzip $outrd1 &
        gzip $outrd2 &
        set +x
        done
done