Merge paired-end FASTQ reads with PANDAseq

merge_paired_end_fastq.sh

#!/bin/bash

set -e

module load PANDAseq/2.11-foss-2016b

find . -name "*_1.fq.gz" | sort -R | while read fwd; do
	rev="${fwd/_1.fq.gz/_2.fq.gz}"
	[[ -s "$rev" ]]

	sample_name="${fwd##*/}"
	sample_name="${sample_name%_1.fq.gz}"
	output="merged/$sample_name.fastq"

	pandaseq -F -w "$output" -f "$fwd" -r "$rev"
done