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