0_merge-fastq.sh

#!/usr/bin/bash

# Specifying Slurm parameters for job submission
#SBATCH -A jknight.prj 
#SBATCH -J fastq-merge 

#SBATCH -o /well/jknight/users/awo868/logs/TAPS-pipeline/merge-fastq_%j.out 

#SBATCH -e /well/jknight/users/awo868/logs/TAPS-pipeline/merge-fastq_%j.err 
#SBATCH -p short 
#SBATCH -c 1 

# Setting default parameter values
input_dir=$PWD
output_dir=$PWD

# Reading in arguments
while getopts i:o:s:h opt
do
	case $opt in
	i)
		input_dir=$OPTARG
		;;
	o)
		output_dir=$OPTARG
		;;
	s)
		sample_list_path=$OPTARG
		;;
	h)
		echo "Usage:	merge-fastq.sh [-i input_dir] [-o output_dir] [-s sample_list_path]"
		echo ""
		echo "Where:"
		echo "-i		Path to input directory containing FASTQ files [defaults to the working directory]"
		echo "-o		Path to output directory where to write merged FASTQ files [defaults to the working directory]"
		echo "-s		Path to a text file containing a list of samples (one sample per line). Sample names should match file naming patterns."
		echo ""
		exit 1
		;;
	esac
done

# Outputing relevant information on how the job was run
echo "------------------------------------------------" 
echo "Run on host: "`hostname` 
echo "Operating system: "`uname -s` 
echo "Username: "`whoami` 
echo "Started at: "`date` 
echo "------------------------------------------------" 

# Validating arguments
echo "[merge-fastq]:	Validating arguments..."

if [[ ! -d $input_dir ]]
then
        echo "[merge-fastq]:	ERROR: Input directory not found."
        exit 2
fi 

if [[ ! -d $output_dir ]]
then
        echo "[merge-fastq]:	ERROR: Output directory not found."
        exit 2
fi 


if [[ ! -f $sample_list_path ]]
then
        echo "[merge-fastq]:	ERROR: Sample list file not found"
        exit 2
fi

# Reading sample list
echo "[merge-fastq]:	Reading sample list..."
readarray sampleList < $sample_list_path


# Parallelising process by sample
sampleName=$(echo ${sampleList[$((${SLURM_ARRAY_TASK_ID}-1))]} | sed 's/\n//g')
echo "[merge-fastq]:	Processing files for sample ${sampleName}..."

# Merging fastq files
file_regex_1="$sampleName*_1.fq.gz"
file_regex_2="$sampleName*_2.fq.gz"

echo "[merge-fastq]:   Merging FASTQ files for read 1..."
zcat ${input_dir}/$file_regex_1 | gzip > ${output_dir}/${sampleName}_1.fastq.gz

echo "[merge-fastq]:   Merging FASTQ files for read 2..."
zcat ${input_dir}/$file_regex_2 | gzip > ${output_dir}/${sampleName}_2.fastq.gz

echo "[merge-fastq]:   ...done!"