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

 

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