Merge branch 'develop' into feature-Chipcap

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala

...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala

...umc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala