Merge branch 'develop' into feature-Chipcap

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

...in/resources/nl/lumc/sasc/biopet/scripts/fastqc_contam.py

...main/resources/nl/lumc/sasc/biopet/scripts/prefixFastq.py

...esources/nl/lumc/sasc/biopet/scripts/pyfastqc/__init__.py

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

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

...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

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

...n/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala

...la/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala

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

...n/scala/nl/lumc/sasc/biopet/scripts/FastqcToContams.scala

.../main/scala/nl/lumc/sasc/biopet/scripts/prefixFastq.scala

.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala

.../main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala

...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala

.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

...st/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala

...ala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala