Fix some issues identified by perlcritic --brutal
Fix some issues identified by perlcritic --brutal

bionitio-team/bionitio,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool,biotool-paper/biotool