Use bash to create a csv file as samplesheet for nextflow

create_input_sheet.sh

# add headers
echo "sample,read1,read2" > input_samplesheet.csv

for read1 in $(ls path/to/directories{1,2,3}/fastq/*_1.{fastq.gz,fq,fq.gz});
    do 
        # get the basename of file and remove suffix
    sample_id=$(echo $read1 | xargs -n 1 basename -s '_1.fastq.gz')
        # replace string '_1' for '_2'
    read2="${read1/_1/_2}"
        # write in a new line for each sample
    echo $sample_id,$read1,$read2 >> input_samplesheet.csv
    done
    
 # with tabs
 echo "sample,read1,read2" > input_samplesheet.csv

for read1 in $(ls path/to/directories{1,2,3}/fastq/*_1.{fastq.gz,fq,fq.gz});
    do 
        # get the basename of file and remove suffix
    sample_id=$(echo $read1 | xargs -n 1 basename -s '_1.fastq.gz')
        # replace string '_1' for '_2'
    read2="${read1/_1/_2}"
        # write in a new line for each sample
    echo -e "$sample_id\t$read1\t$read2" >> input_samplesheet.csv