Merge branch 'develop' into feature-fixed_values

external-example/.gitignore

external-example/README.md

external-example/pom.xml

.../src/main/scala/org/example/group/ExecutableExample.scala

...in/scala/org/example/group/pipelines/BiopetPipeline.scala

...ala/org/example/group/pipelines/MultisamplePipeline.scala

...in/scala/org/example/group/pipelines/SimplePipeline.scala

pom.xml

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

.../lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

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

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

...scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala

...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

...s/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp

...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp