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?