Conflicts:
	flexiprep/nbactions.xml
	gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
	gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
	mapping/examples/test.json
	mapping/nbactions.xml
	pom.xml

removing source files from jar packaging

- Added a mapping module (not yet used in Gatk)
- Added VariantRecalibrator to Gatk