Merge branch 'feature-gentrap_additions' into 'develop'

Feature gentrap additions

This is the latest updates and fixes on the Gentrap pipeline to be compatible with the most recent framework updates.

In particular:

* Issue #156 is fixed ~ this was due to class initialization problems
* Issue #157 is fixed
* TopHat alignment results are now merged with its unmapped alignment file, producing the correct statistics
* The pipeline is updated with the new reference module.
* Redundant CollectRnaSeqMetrics is removed (now using the one from BamMetrics instead).

See merge request !181