Merge remote-tracking branch 'remotes/origin/develop' into feature-general-refactor-biopet
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- docs/pipelines/shiva.md 11 additions, 0 deletionsdocs/pipelines/shiva.md
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala 12 additions, 5 deletions.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala 2 additions, 2 deletions.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala
- public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala 2 additions, 2 deletions.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala 150 additions, 2 deletions...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala 3 additions, 0 deletions.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala 6 additions, 1 deletion...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala 1 addition, 1 deletion.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
- public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickClosedReferenceOtus.scala 2 additions, 2 deletions...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala
- public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp 23 additions, 2 deletions...c/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp
- public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala 2 additions, 2 deletions...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
- public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Freebayes.scala 2 additions, 9 deletions...asc/biopet/pipelines/shiva/variantcallers/Freebayes.scala
- public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala 11 additions, 8 deletions...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
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