diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
index 179c5e02a31ef4fda14a828e623850afec7429ec..b82cc87fea6cf35287bef1ccff07ac7ad1559922 100644
--- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
+++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
@@ -33,7 +33,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
    * @param script name / location of script
    */
   def setPythonScript(script: String) {
-    pythonScript = new File(script)
+    pythonScript = new File(script).getAbsoluteFile
     if (!pythonScript.exists()) {
       setPythonScript(script, "")
     } else {
@@ -48,7 +48,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
    */
   def setPythonScript(script: String, subpackage: String) {
     pythonScriptName = script
-    pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName)
+    pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName).getAbsoluteFile
     if (!pythonScript.getParentFile.exists) pythonScript.getParentFile.mkdirs
     val is = getClass.getResourceAsStream(subpackage + pythonScriptName)
     if (is != null) {