azmigueldario

# 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

azmigueldario

LINES=100
INPUT_FILE='PATH/TO/TEXT/CSV'

tail -n +2 $INPUT_FILE | split -l $LINES - prefix_

for file in prefix_*
do
    head -n 1 $INPUT_FILE > tmp_file
    cat $file >> tmp_file
    mv -f tmp_file $file