Merge fastq files from multiple lanes using shell script

merge_fastq.sh

#!/bin/bash
# $1 is PATH
args=("$@")
input_dir=${args[0]}
output_dir=${args[1]}

main() {
    set -e -x -o pipefail
    # get R1
    declare -a fastq1=($(ls -d $input_dir/*R1*.fastq.gz))    #($(ls *_R1_001.fastq.gz))
    declare -a fastq2=($(ls -d $input_dir/*R2*.fastq.gz))    #($(ls *_R2_001.fastq.gz))

    # sanity-check inputs
    pairs="${#fastq1[@]}"
    if [ "$pairs" -ne "${#fastq2[@]}" ]; then
        echo "fastq1 and fastq2 input arrays have different lengths. The fastq1 input array should contain the 'left' read files, and the fastq2 input array should contain the 'right' read files.";
        exit 1
    fi
    # Get name of 1st file within fastq1 array
    name="${fastq1[0]}"

    # Strip suffixes from filename to obtain sample_name
    if [ "$sample_name" == "" ]; then
        sample_name=${name%.gz}
        sample_name=${sample_name%.fastq}
        sample_name=${sample_name%.1}
        sample_name=${sample_name%_1}
        sample_name=${sample_name%.001}
        sample_name=${sample_name%_001}
        sample_name=${sample_name%.R1}
        sample_name=${sample_name%_R1}
        sample_name=${sample_name%.R2}
        sample_name=${sample_name%_R2}
    fi

    # Assign output name
    fastq1_outfile="${sample_name}_merged_R1_001.fastq.gz"
    fastq2_outfile="${sample_name}_merged_R2_001.fastq.gz"
    # remove prefix
    fastq1_outfile=$output_dir/"${fastq1_outfile#$input_dir}"
    fastq2_outfile=$output_dir/"${fastq2_outfile#$input_dir}"
    echo $fastq1_outfile
    echo $fastq2_outfile

    if [[ $name =~ \.gz$ ]]; then
        # gzipped files, can be concat-ed without decompression
        cat "${fastq1[@]}" > $fastq1_outfile
        cat "${fastq2[@]}" > $fastq2_outfile
    else
        # non-gzipped, assume no compression currently
        cat "${fastq1[@]}" | bgzip -c > $fastq1_outfile
        cat "${fastq2[@]}" | bgzip -c > $fastq2_outfile
    fi
    echo Done merging files!!!
}
main input_dir output_dir
               

USAGE: ./merge_fastq.sh input_dir output_dir

time sh merge_fastq.sh path_to_fastq . >& m.log