Merge branch 'fix-tools_mainclass' into 'develop'

Fixed bug in loading the mainClass for biopet tools

Fixes a small bug in loading the mainClass of tools.

When jenkins don't complain this can be merged.

See merge request !281

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
 
 class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
-  val builder = BammetricsReport
+  def builder = BammetricsReport
 }
 
 /**

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala

@@ -13,8 +13,5 @@ trait ToolCommandFunction extends BiopetJavaCommandLineFunction with Version {
 
   override def getVersion = Some("Biopet " + FullVersion)
 
-  override def beforeGraph(): Unit = {
-    javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
-    super.beforeGraph()
-  }
+  javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
 }

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -33,7 +33,7 @@ import scala.collection.mutable
 trait ReportBuilderExtension extends ToolCommandFunction {
 
   /** Report builder object */
-  val builder: ReportBuilder
+  def builder: ReportBuilder
 
   def toolObject = builder
 

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala

@@ -12,8 +12,8 @@ class ToolCommandTest extends TestNGSuite with Matchers {
   @Test
   def testToolCommand: Unit = {
     val tool = new ToolCommandFunction {
-      val root = null
-      val toolObject = ToolCommandTest
+      def root = null
+      def toolObject = ToolCommandTest
     }
 
     tool.versionCommand shouldBe empty

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala

@@ -26,7 +26,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
  * Created by pjvanthof on 25/06/15.
  */
 class CarpReport(val root: Configurable) extends ReportBuilderExtension {
-  val builder = CarpReport
+  def builder = CarpReport
 }
 
 object CarpReport extends MultisampleReportBuilder {

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
 import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
 
 class FlexiprepReport(val root: Configurable) extends ReportBuilderExtension {
-  val builder = FlexiprepReport
+  def builder = FlexiprepReport
 }
 
 /**

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala

@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.core.report._
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class GearsReport(val root: Configurable) extends ReportBuilderExtension {
-  val builder = GearsReport
+  def builder = GearsReport
 }
 
 object GearsReport extends ReportBuilder {

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala

@@ -26,7 +26,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
  * Created by pjvanthof on 25/06/15.
  */
 class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
-  val builder = GentrapReport
+  def builder = GentrapReport
 }
 
 object GentrapReport extends MultisampleReportBuilder {

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala

@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
 
 class MappingReport(val root: Configurable) extends ReportBuilderExtension {
-  val builder = MappingReport
+  def builder = MappingReport
 }
 
 /**

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -30,7 +30,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
  * Created by pjvan_thof on 3/30/15.
  */
 class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
-  val builder = ShivaReport
+  def builder = ShivaReport
 }
 
 /** Object for report generation for Shiva pipeline */