Merge remote-tracking branch 'remotes/origin/develop' into fix-Shiva_bcftools_calling

biopet-aggregate/copy-src.sh

biopet-aggregate/pom.xml

biopet-aggregate/rm-src.sh

biopet-aggregate/src/.gitignore

pom.xml

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

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

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

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

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

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

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

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

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

...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala

...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

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

...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala