Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs.  Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list. 

Instead, I have a list of dataset pairs (for paired-end data).  This cannot be provided to bowtie as input.  If I correct this, should I create a pull request for it?  Alternatively, does someone already have a corrected version of this?

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