Hello, We noticed a problem with the tool Filter Fastq. It seemed to mishandle the paired-end checkbox. Here is the XML which seems to not work: <param name="paired_end" label="This is paired end data" type="boolean" truevalue="paired_end" falsevalue="single_end" checked="False"/> Concretely, $paired_end.value return True or False as value and not "paired_end" or "single_end", so in the python code execution, #if $paired_end.value == 'single_end': qual_scores_split = [ qual_scores ] #else: qual_scores_split = [ qual_scores[ 0:int( len( qual_scores ) / 2 ) ], qual_scores[ int( len( qual_scores ) / 2 ): ]] Always go in the else, always splitting reads even when they are single_end. It induces wrong results in our read filtering. I hope the explanation is clear enough Best regards, Felix