Merge branch 'develop' into fix-BIOPET-582

Jenkinsfile

README.md

bam2wig/pom.xml

bammetrics/pom.xml

basty/pom.xml

...scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

biopet-core/pom.xml

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

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

...rc/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

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

...t/scala/nl/lumc/sasc/biopet/core/PipelineStatusTest.scala

.../nl/lumc/sasc/biopet/core/annotation/AnnotationTest.scala

biopet-extensions/pom.xml

...ces/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.py

...c/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala

...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala

...l/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala

...sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala

...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala