chapmanb/bcbio-nextgen — pull request #150 by porterjamesj (2013-10-27 00:03:17+00:00)
Title: Have tophat get transcriptome index or GTF file from genome-resources yaml.

I noticed that tophat was ignoring some information in genome-resources.yaml, so I decided to fix it.

This required passing all the aligners the whole `data` dictionary, rather than just `data["config"]`. This allows them to access more information; e.g. the genome-resources. I used this to make tophat get the reference transcriptome and transcriptome index from here, rather than the hardcoded paths that it used previously. This also paves the way for other aligners to make use of this information if possible in the future.

The tests all passed, but the suite isn't comprehensive, I had to change the signature for all the aligners and I may have missed some entry points. Its probably best for someone more familiar with this code to go through my changes carefully before merging.

Also note that this a breaking change for anyone who's depending on the hardcoded paths and doesn't have their genome-resources files set up correctly.