Use combine resources for pipes

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

@@ -70,6 +70,10 @@ class BiopetFifoPipe(val root: Configurable,
       fifosFiles.map(required("rm", _)).mkString("\n\n", " \n", " \n\n") +
       BiopetFifoPipe.endScript
   }
+
+  override def setResources(): Unit = {
+    combineResources(commands)
+  }
 }
 
 object BiopetFifoPipe {

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

@@ -45,6 +45,10 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
     require(inputOutput.isEmpty, "File found as input and output in the same job, files: " + inputOutput.mkString(", "))
   }
 
+  override def setResources(): Unit = {
+    combineResources(pipesJobs)
+  }
+
   override def defaultCoreMemory = 0.0
   override def defaultThreads = 0