Merge commit 'cfae9015'
Conflicts: flexiprep/nbactions.xml gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala mapping/examples/test.json mapping/nbactions.xml pom.xml
bam-metrics/pom.xml
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