diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
index a1ce42408cf1ffe69ac3d1a3b92db8ead9de2f71..fa177b8fe4cd52cfee1307dbb4e9aeeb5ded4e08 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
@@ -23,6 +23,7 @@ import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 import scala.io.Source
 
+/** Extension for md5sum */
 class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input")
   var input: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
index 03f76abd6162f5759fb772158a5f1dc941012b1c..6756c5eafc7ab5b9a3ba1fd60fc89154bc0aa0df 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for pbzip2 */
 class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Zipped file")
   var input: File = _
@@ -39,6 +40,7 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
     if (!memory.isEmpty) memory = Option(memory.get * threads)
   }
 
+  /** return commandline to execute */
   def cmdLine = required(executable) +
     conditional(decomrpess, "-d") +
     conditional(!decomrpess, "-z") +
@@ -48,7 +50,9 @@ class Pbzip2(val root: Configurable) extends BiopetCommandLineFunction {
     required(input)
 }
 
+/** Object for constructors for Pbzip2 */
 object Pbzip2 {
+  /** Default constructor */
   def apply(root: Configurable, input: File, output: File): Pbzip2 = {
     val pbzip2 = new Pbzip2(root)
     pbzip2.input = input
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
index ebfaac812bbedec10a14d0daad609d54469f9c03..cf088cb29fa57d66b1fb9fe24b247054e0ae2edc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
@@ -28,6 +28,11 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   executable = config("exe", default = "python", submodule = "python")
 
   protected var python_script_name: String = _
+
+  /**
+   * checks if script already exist in jar otherwise try to fetch from the jar
+   * @param script name / location of script
+   */
   def setPythonScript(script: String) {
     python_script = new File(script)
     if (!python_script.exists()) {
@@ -36,6 +41,12 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
       python_script_name = script
     }
   }
+
+  /**
+   * Set and extract python script from jar file
+   * @param script name of script in jar
+   * @param subpackage location of script in jar
+   */
   def setPythonScript(script: String, subpackage: String) {
     python_script_name = script
     python_script = new File(".queue/tmp/" + subpackage + python_script_name)
@@ -46,6 +57,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
     os.close()
   }
 
+  /** return basic command to prefix the complete command with */
   def getPythonCommand(): String = {
     required(executable) + required(python_script)
   }