Merge branch 'develop' into feature-unittest_core
Conflicts: public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
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- docs/config.md 5 additions, 5 deletionsdocs/config.md
- protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala 1 addition, 1 deletion...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
- protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala 2 additions, 2 deletions...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala 11 additions, 11 deletions...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala 1 addition, 1 deletion.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala 7 additions, 7 deletions...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 40 additions, 7 deletions...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 10 additions, 10 deletions...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala 4 additions, 4 deletions...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala 4 additions, 11 deletions.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala 19 additions, 21 deletions...lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 30 additions, 16 deletions...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala 3 additions, 0 deletions...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala 3 additions, 3 deletions...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala 1 addition, 1 deletion...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala 1 addition, 1 deletion...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala 1 addition, 1 deletion...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala 1 addition, 1 deletion...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
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