Safer class name, now checked by the compiler

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 = _

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 = _

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 = _

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

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

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

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

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

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

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

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 = _

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 = _