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

biopet-aggregate/pom.xml

docs/developer/example-pipeline.md

docs/general/memory.md

docs/pipelines/basty.md

docs/pipelines/shiva.md

...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

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

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

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

...scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala

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

...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

...sc/biopet/core/extensions/PythonCommandLineFunction.scala