Feature core unit tests

Fixes #253 

See merge request !307

Fix renames

Some naming fixes for consistency.

See merge request !309

Feature basic gentrap report

Part of #223 

This only contains basic stats, no gentrap specific stats added.

See merge request !302

Fix spelling error in the WriteDependencies JSON output

Fix the output keys for the JSON output of `writedependencies`.

See merge request !305

Fix short name



See merge request !303

Switch gentrap to multisample mapping

Fixes #256 

See merge request !299

Feature varda

fixes #208 

This is to track this branch in jenkins

See merge request !245

Fix output file for tophat step

Still needs testing

See merge request !300