What Bjoern said - unless you meant the older bowtie1 wrappers. Those have not been updated - I think we decision was made at Penn State to focus on bowtie2 - but if people are still interested in enhancing the bowtie1 wrappers I think a PR would be welcome. There have been some other relatively recent bowtie1 PRs (e.g. from Nicola https://github.com/galaxyproject/tools-devteam/pull/49).
-John
On Thu, Jun 25, 2015 at 3:46 AM, Bjoern Gruening bjoern.gruening@gmail.com wrote:
Hi Ryan,
latest wrappers are here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 And a PR would be great!
But as far as I can see this is already implemented and you can choose as option `Paired-end Dataset Collection`, isn't it?
Ciao, Bjoern
On 24.06.2015 20:02, Ryan G wrote:
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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