diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RscriptCommandLineFunction.scala
similarity index 84%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
rename to public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RscriptCommandLineFunction.scala
index d666fa377149c0103c7900fe2555fb0c03226e96..391514a395eb1d86de24accedf99d410fe6a40dc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RscriptCommandLineFunction.scala
@@ -4,13 +4,12 @@
  * @author  Wibowo Arindrarto
  */
 
-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
+
+import java.io.{File, FileOutputStream}
 
-import java.io.FileOutputStream
-import java.io.File
-import org.broadinstitute.gatk.utils.commandline.{ Input }
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import scala.collection.JavaConversions._
+import org.broadinstitute.gatk.utils.commandline.Input
 
 /**
  * Trait for RScript wrappers
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
index 7c6ab60c56716956eb723332add72dc4c9237a77..21b745a7a09d7aa8113444255d7ff331383e9c10 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
@@ -9,7 +9,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
index 6398ceefc97b4ad2c5abd4c8e1934afd7ccfc370..fefd3b9a05fc14e37cb76462a9846875a4f4a0a5 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
@@ -9,7 +9,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
index f9acc767374f4347e6ca552c2f8c03f36d321e03..b82cca7a8084720823bd705ad1ec79148cfcdbd8 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
@@ -9,7 +9,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RScriptCommandLineFunction
+import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**