Merge branch 'feature-improve_multisample' into 'develop'

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

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

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

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

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

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

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

...c/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

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

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

...mc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala