diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
index 667e3ce6731bcb0ae453390d9259cc0fe8704b41..3d5c86085c4b257e5d1dd0b64df9ef1be640ed02 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
@@ -6,5 +6,12 @@ import nl.lumc.sasc.biopet.FullVersion
  * Created by pjvanthof on 11/09/15.
  */
 trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
+  def toolObject: Object
+
   override def getVersion = Some("Biopet " + FullVersion)
+
+  override def freezeFieldValues(): Unit = {
+    javaMainClass = toolObject.getClass.getName.split("$").head
+    super.freezeFieldValues()
+  }
 }
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
index 846dc2323b38aba544318a171bab10233d1a2cee..9b0020ae21e8626f3f987aaec2d1bd2921374bed 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BastyGenerateFasta.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BastyGenerateFasta
 
   @Input(doc = "Input vcf file", required = false)
   var inputVcf: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
index 7f76526fc4404d93ab71b970aaff7b1071b54b61..bab2f7c0ae0fa260a78ff366d9e9f4a6c177d9f6 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * @deprecated Use picard.util.BedToIntervalList instead
  */
 class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BedToInterval.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BedToInterval
 
   @Input(doc = "Input Bed file", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
index 104674cdff2ecdd9002165c15fa4c6ebb7f1c7fb..817b6d3f2792168a8f4fdf8549fa3c16c858e21e 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
 
   @Input(doc = "Input fasta", shortName = "input", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
index 3692244ae114ebf479cd31cb9b86dfc431a850cb..ff06bc963764f07563aa4ca0e2926119ba667c9b 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
-  javaMainClass = nl.lumc.sasc.biopet.tools.BiopetFlagstat.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.BiopetFlagstat
 
   @Input(doc = "Input bam", shortName = "input", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
index 8bbd7e06720b521245bb311af98b12ea1000a0d5..df7e32e19bacfc8021ec015fcf019f9f16f61fe2 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * @param root Parent object
  */
 class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.FastqSplitter.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.FastqSplitter
 
   @Input(doc = "Input fastq", shortName = "input", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
index ff67f5777bb069adf3abdbf6a53ebe47f968cb8d..90100c8e7942afe8dd105ca64ba2ff5990747b7f 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
@@ -32,7 +32,7 @@ import scala.util.matching.Regex
  */
 class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
 
-  javaMainClass = nl.lumc.sasc.biopet.tools.FastqSync.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.FastqSync
 
   @Input(doc = "Original FASTQ file (read 1 or 2)", shortName = "r", required = true)
   var refFastq: File = null
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
index 3933892ff127fba05c62aee3158b1d78b8bb7d3b..eedb51fdd1bb9d07d405299cb9dbf913681fbb96 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.MergeAlleles.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.MergeAlleles
 
   @Input(doc = "Input vcf files", shortName = "input", required = true)
   var input: List[File] = Nil
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
index 7845639b6fa39ef2272801fc00e38f56cf48e45c..96a421db3e706d0220df76b6acfd5aab9cda9480 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
@@ -30,7 +30,7 @@ import scala.collection.mutable.{ Set => MutSet }
  */
 class MergeTables(val root: Configurable) extends ToolCommandFuntion {
 
-  javaMainClass = nl.lumc.sasc.biopet.tools.MergeTables.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.MergeTables
 
   override def defaultCoreMemory = 6.0
 
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index c40754a2d0af180dfbd84e864bf615cc4234f622..5a3e1e3f26588c103a4bf5e0a190aa223d064450 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.JavaConversions._
 
 class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
-  javaMainClass = nl.lumc.sasc.biopet.tools.MpileupToVcf.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.MpileupToVcf
 
   @Input(doc = "Input mpileup file", shortName = "mpileup", required = false)
   var inputMpileup: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
index 4ab27f0588e51c7630600c1e061e60ac981b39e9..302aa11586119a6602f29b0b452ed0645aeb2c37 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
  * Created by pjvan_thof on 1/13/15.
  */
 class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.PrefixFastq.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.PrefixFastq
 
   override def defaultCoreMemory = 1.0
 
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
index d0d9fa73929467e261a81f2f328013af66c5a794..2ee9d97e17ef35cbf6573bf0fa91bb5fc8f76b2c 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SageCountFastq.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SageCountFastq
 
   @Input(doc = "Input fasta", shortName = "input", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
index 1bf0b0f55015d292e74333cf412c231674946d04..4b287d2cefaf98c777ca2ad44084f74bfacf5047 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SageCreateLibrary.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SageCreateLibrary
 
   @Input(doc = "Input fasta", shortName = "input", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
index d94e9106ed92c069dbfb8b576f92af38e549a8bf..d0779973b4484f29264bc574af6d898e1df8804d 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SageCreateTagCounts.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SageCreateTagCounts
 
   @Input(doc = "Raw count file", shortName = "input", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
index cbe915cf04d938d00fae9f2409039237bf549fd9..cc7a8e6ede5bb1ba0d318639e8b9320a0ae8024a 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
@@ -14,7 +14,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  * @param root Configuration object for the pipeline
  */
 class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SeqStat.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SeqStat
 
   @Input(doc = "Input FASTQ", shortName = "input", required = true)
   var input: File = null
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
index e20b2822a38f6b8260785abcf00105473cd242b4..558c93f8532b95ccd3dfa33e3265f0fbebda8104 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Created by pjvanthof on 22/08/15.
  */
 class SquishBed(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.SquishBed.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.SquishBed
 
   @Input(doc = "Input Bed file", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
index 6884f0788a2c72c7a2b0d4ed32cb5e3cf48ccdd2..60d550532dfd30150e63f11096237356aa182a1a 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VcfFilter.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VcfFilter
 
   @Input(doc = "Input vcf", shortName = "I", required = true)
   var inputVcf: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
index 15fe27c04e4d5f2db7595043407431263c2f6d9a..3fd09a67fb74b3759ec3f00c51344f88afc53231 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
@@ -30,7 +30,7 @@ import scala.io.Source
  * Created by pjvan_thof on 1/10/15.
  */
 class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VcfStats.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VcfStats
 
   @Input(doc = "Input fastq", shortName = "I", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
index c3438ff4d529e741c9fb213457a194e6392f6262..5ab877502eaef6133b51a1927c83b94dc5b7b3ba 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  * Biopet extension for tool VcfWithVcf
  */
 class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VcfWithVcf.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VcfWithVcf
 
   @Input(doc = "Input vcf file", shortName = "input", required = true)
   var input: File = _
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
index cb71ee26c0d9a80f092979c8fbf3812dec885262..4379b990dd585b012b15a44a7fc0605a7772b898 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
@@ -32,7 +32,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  */
 
 class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
-  javaMainClass = nl.lumc.sasc.biopet.tools.VepNormalizer.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.VepNormalizer
 
   @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
   var inputVCF: File = null
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
index 9c892245c37a4be4c66c83906a8483d5d03968a5..1e468bd36ac52bed889ccc0871a092316def63f0 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
@@ -29,7 +29,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  */
 class WipeReads(val root: Configurable) extends ToolCommandFuntion {
 
-  javaMainClass = nl.lumc.sasc.biopet.tools.WipeReads.getClass.getName
+  def toolObject = nl.lumc.sasc.biopet.tools.WipeReads
 
   @Input(doc = "Input BAM file (must be indexed)", shortName = "I", required = true)
   var inputBam: File = null