This script can map(bowtie2) paied-end dataset(s) to a referenece sequence and automatically removes soft clipped reads from the sam file using samclip
nextflow run AgBC-UoP/mapNclean-nf --reads {readDir/READ_PATTERN} --reference {referenceDir/ref.fa}
ex : nextflow run AgBC-UoP/mapNclean-nf --reads "*R{1,2}*.fastq" --reference refseq.fa