Merge branch 'develop' into feature-fastq_sync

...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

...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

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

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

...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

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