Multisample mapping pipeline

Fixes #225 

See merge request !292

Added gender and groups to samples

Fix for #131 

See merge request !296

Feature generate indexes

see also #187 

See merge request !211

Added unit tests to reference trait

Fixes #250

Also implemented improved test aggregation

See merge request !298

Fixed scattering



See merge request !295

Conflicts:
	public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

(cherry picked from commit d88e0815)