Fix on exe

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala

 package nl.lumc.sasc.biopet.core
 
-trait BiopetExecutableProtected extends BiopetExecutablePublic {
-  override def pipelines: List[MainCommand] = super.pipelines ::: List(
+object BiopetExecutableProtected extends BiopetExecutable {
+  def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(
     nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
@@ -9,4 +9,6 @@ trait BiopetExecutableProtected extends BiopetExecutablePublic {
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare,
     nl.lumc.sasc.biopet.pipelines.basty.Basty)
-}
+  
+  def tools = BiopetExecutablePublic.tools
+}
\ No newline at end of file

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

 package nl.lumc.sasc.biopet.core
 
-trait BiopetExecutablePublic extends BiopetExecutable {
+object BiopetExecutablePublic extends BiopetExecutable {
   def pipelines: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
     nl.lumc.sasc.biopet.pipelines.mapping.Mapping,