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Merge branch 'feature-cnvpipeline' into 'develop'
Feature cnvpipeline - including changing the PythonCommandLineFunction CNV pipeline - starts with bamfile Tickets: #106 #107 Work for KG See merge request !76
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- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala 8 additions, 1 deletion...mc/sasc/biopet/extensions/PythonCommandLineFunction.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala 34 additions, 0 deletions...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala 49 additions, 0 deletions.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala 35 additions, 0 deletions.../nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala 39 additions, 0 deletions...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
- public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala 40 additions, 0 deletions.../nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
- public/biopet-public-package/pom.xml 5 additions, 0 deletionspublic/biopet-public-package/pom.xml
- public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala 2 additions, 1 deletion...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
- public/kopisu/.gitignore 1 addition, 0 deletionspublic/kopisu/.gitignore
- public/kopisu/pom.xml 43 additions, 0 deletionspublic/kopisu/pom.xml
- public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala 121 additions, 0 deletions...l/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
- public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala 65 additions, 0 deletions...nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
- public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala 56 additions, 0 deletions...n/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
- public/pom.xml 2 additions, 1 deletionpublic/pom.xml
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