Merge commit '3daaba4b' into feature-sample_config_create

biopet-framework/BiopetFramework.iml

biopet-framework/examples/shark_apps.json

biopet-framework/nb-configuration.xml

biopet-framework/pom.xml

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

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

...ork/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala

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

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

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

...rk/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

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

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

...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

...scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala

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

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

...umc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala

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

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