<command interpreter="bash">

seqclust-main.sh -s $input -m $mvstup -o $ovstup -d $repeatmasker -v $archive -w $contigs -y $log -x pdffile.pdf -z RMSKtable -r $__root_dir__ -t $summary -u '$summary.extra_files_path' -p $paired -f $prefix -a $sq_rename -l $overlap