add filtering/required flags
add filtering/required flags

PeteHaitch/bwa-parclip,dariober/bwa-meth,dariober/bwa-meth,PeteHaitch/bwa-parclip,dariober/bwa-meth,brentp/bwa-meth,PeteHaitch/bwa-parclip,brentp/bwa-meth,brentp/bwa-meth