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?