diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
similarity index 96%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
index 59e4ed04c39f66e88e2f02fc0fde9b954d3efa5e..000c77a9acd18080b77b4d34029bf95d6064ab71 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
@@ -13,9 +13,9 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.core.extensions
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.Input
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
similarity index 96%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
index cd45ff92b557b7be4f5fa8ca76030f8b8a2babaf..cce714ef1eb96a002748f0ea3aa0d2148a588426 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
@@ -13,9 +13,9 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.core.extensions
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
index 01b78279ca78d9f7f899445a971fc5a19bd775c1..5174f66af523bf5fd3b84ade4d0cc49ce1903946 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
index 7d061ed819bc91c8d0fa641783ff89a50e58bd6f..1488cabc468071702f4b2c748e2a2363dac9d810 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions.conifer
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
abstract class Conifer extends PythonCommandLineFunction {
override def subPath = "conifer" :: super.subPath
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
index 373bf282ac44a94ba8a0f890c6a33bc35f844cb5..4ff413b1f8b0c9a32929c36902327eb3a891565b 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
index 58c3e7c534286dceefe4bfd6c17bf9424942b81a..ad3533ced93e6e43da95d2cab717c8c48c39d426 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
index 7a1d4a36b4ee8096c8671a882ef24c18655820e9..2bf533f81feed33a5c840a341376b9776c502c47 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
index 5aedfa0016be0b608b3a51abf0d7149b058f4965..79ab04b94d3f0befafabada3c0fd77f1471ceaa7 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.scripts
import java.io.File
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }