Merge remote-tracking branch 'remotes/origin/develop' into feature-gatk_et_option

Conflicts:
	protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala