no more failing tests :-)
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- docs/developer/example-pipeline.md 1 addition, 1 deletiondocs/developer/example-pipeline.md
- docs/pipelines/basty.md 2 additions, 2 deletionsdocs/pipelines/basty.md
- docs/pipelines/shiva.md 1 addition, 1 deletiondocs/pipelines/shiva.md
- protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala 1 addition, 1 deletion...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
- public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala 2 additions, 2 deletions...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala 1 addition, 1 deletion...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala 1 addition, 1 deletion...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala 2 additions, 2 deletions...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala 1 addition, 1 deletion...sc/biopet/core/extensions/PythonCommandLineFunction.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala 1 addition, 1 deletion.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala 1 addition, 1 deletion.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala 1 addition, 1 deletion...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala 1 addition, 1 deletion...in/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala 1 addition, 1 deletion...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
- public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala 1 addition, 1 deletion...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
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