Merge branch 'develop' into feature-wipereads

biopet-framework/nb-configuration.xml

biopet-framework/pom.xml

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

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

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

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

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

...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

...la/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala

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

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

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

...rk/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

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

...cala/nl/lumc/sasc/biopet/extensions/aligners/Bowtie.scala

.../scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala

...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

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