setupRetry calls setupretry of pipe functions

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

@@ -74,6 +74,12 @@ class BiopetFifoPipe(val root: Configurable,
   override def setResources(): Unit = {
     combineResources(commands)
   }
+
+  override def setupRetry(): Unit = {
+    super.setupRetry()
+    commands.foreach(_.setupRetry())
+    combineResources(commands)
+  }
 }
 
 object BiopetFifoPipe {

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

@@ -49,6 +49,12 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
     combineResources(pipesJobs)
   }
 
+  override def setupRetry(): Unit = {
+    super.setupRetry()
+    commands.foreach(_.setupRetry())
+    combineResources(commands)
+  }
+
   override def defaultCoreMemory = 0.0
   override def defaultThreads = 0