Merge branch 'feature-scaliform-maven' into 'develop'
Feature scaliform maven + Add scaliform maven plugin - Removed config for Netbeans, not using the CheckStyle plugin anymore See merge request !24
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- biopet-framework/nb-configuration.xml 0 additions, 1 deletionbiopet-framework/nb-configuration.xml
- biopet-framework/pom.xml 34 additions, 0 deletionsbiopet-framework/pom.xml
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 3 additions, 3 deletions...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala 4 additions, 4 deletions...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 1 addition, 1 deletion...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala 6 additions, 6 deletions...n/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 3 additions, 3 deletions...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 6 additions, 8 deletions...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala 33 additions, 29 deletions...src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala 8 additions, 8 deletions...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala 2 additions, 2 deletions...la/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala 9 additions, 9 deletions.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala 2 additions, 2 deletions...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 3 additions, 3 deletions...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala 9 additions, 9 deletions...rk/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala 36 additions, 37 deletions...c/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bowtie.scala 2 additions, 2 deletions...cala/nl/lumc/sasc/biopet/extensions/aligners/Bowtie.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala 2 additions, 2 deletions.../scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala 2 additions, 2 deletions...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
- biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala 2 additions, 2 deletions.../lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
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