diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
index 232cbc24123983bc46f7c51f98284be10bb6f2a8..bd1c2ff70b864c275d8b491073eee6ed0485813f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard AddOrReplaceReadGroups */
 class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
-  javaMainClass = "picard.sam.AddOrReplaceReadGroups"
+  javaMainClass = new picard.sam.AddOrReplaceReadGroups().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
index 314418afac041354b0782e2a0d95be8474f6fcce..7eb26f2371ad3b6e41882321fcc4355cc11692e4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard CalculateHsMetrics */
 class CalculateHsMetrics(val root: Configurable) extends Picard {
-  javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
+  javaMainClass = new picard.analysis.directed.CalculateHsMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index 541ee75b88a3d9f9b2111b81ee69fc11665b205d..66697a0b247fdf24a7bf3c5016c4c7612f4b39fb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard CollectAlignmentSummaryMetrics */
 class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
-  javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
+  javaMainClass = new picard.analysis.CollectAlignmentSummaryMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index f93dc4aa77241dabfee7c0703536fda9cb6afa2c..c1197cc21a3e7a8296a6e66075147fc1c12a2ad7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard CollectGcBiasMetrics */
 class CollectGcBiasMetrics(val root: Configurable) extends Picard {
-  javaMainClass = "picard.analysis.CollectGcBiasMetrics"
+  javaMainClass = new picard.analysis.CollectGcBiasMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: Seq[File] = Nil
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index 6ef7bd62e304a63f913aa154077dfda80211077f..bfe20ec897f0fbe6a4fab03469433f10cf3e3a32 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -24,7 +24,7 @@ import scala.collection.immutable.Nil
 
 /** Extension for picard CollectInsertSizeMetrics */
 class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
-  javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
+  javaMainClass = new picard.analysis.CollectInsertSizeMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: File = null
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
index 6629fae64d63241b95c164c9adad8003e5437ad8..dd922fce5b40b6063806db87964f578a1f03499f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
@@ -26,7 +26,7 @@ import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
  */
 class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summarizable {
 
-  javaMainClass = "picard.analysis.CollectRnaSeqMetrics"
+  javaMainClass = new picard.analysis.CollectRnaSeqMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze", required = true)
   var input: File = null
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
index 89ceb13e3675999a8a0637986cc7e162640edc23..1d7671a4fd0f67cce3eeab7f2076f6f0dfdf6231 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 
 class GatherBamFiles(val root: Configurable) extends Picard {
 
-  javaMainClass = "picard.sam.GatherBamFiles"
+  javaMainClass = new picard.sam.GatherBamFiles().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: List[File] = Nil
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 52777a46742dbe7c62a00422edf36585be72b010..318b1e7f44e3ad40c197668fa2dec6cd52f0fcc5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -22,7 +22,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard MarkDuplicates */
 class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
-  javaMainClass = "picard.sam.MarkDuplicates"
+
+  javaMainClass = new picard.sam.MarkDuplicates().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
   var input: List[File] = Nil
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
index ef3f358ab1598680a5f7b1fcb690232dd020bbe6..3c850f374114e1b357c823dbb5cccce7da00e28f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard MergeSamFiles */
 class MergeSamFiles(val root: Configurable) extends Picard {
-  javaMainClass = "picard.sam.MergeSamFiles"
+  javaMainClass = new picard.sam.MergeSamFiles().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: List[File] = Nil
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
index cb29b2e1e9ea1816615c14ef279b920d7ecc172f..f90a089383ba57d84fdefab3645451c829668b89 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 
 class ReorderSam(val root: Configurable) extends Picard {
 
-  javaMainClass = "picard.sam.ReorderSam"
+  javaMainClass = new picard.sam.ReorderSam().getClass.getName
 
   @Input(doc = "Input SAM or BAM file", required = true)
   var input: File = null
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index 96bfdf4223851b83d137a066cfbf3df8d222659e..d997e472f9bde0244a6c05bfd8fd3aaefa1ad3ec 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard SamToFastq */
 class SamToFastq(val root: Configurable) extends Picard {
-  javaMainClass = "picard.sam.SamToFastq"
+  javaMainClass = new picard.sam.SamToFastq().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 8d2946291928f4019c52e1cdc7b6bf52c00df89a..fecc71075c25f129081de5d89dc3e41d8fb94b05 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 /** Extension for picard SortSam */
 class SortSam(val root: Configurable) extends Picard {
-  javaMainClass = "picard.sam.SortSam"
+  javaMainClass = new picard.sam.SortSam().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: File = _