Remove addSummaryJobs()

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

@@ -133,12 +133,11 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
       case that: SummaryQScript =>
         that.init()
         that.biopetScript()
-        that.addSummaryJobs()
         this match {
           case s: SummaryQScript => s.addSummaryQScript(that)
           case _ =>
         }
-      case that:BiopetQScript =>
+      case that: BiopetQScript =>
         that.init()
         that.biopetScript()
       case _ => subPipeline.script

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

@@ -92,8 +92,11 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
     summaryQScripts :+= summaryQScript
   }
 
+  private var addedJobs = false
+
   /** Add jobs to qscript to execute summary, also add checksum jobs */
   def addSummaryJobs(): Unit = {
+    if (addedJobs) throw new IllegalStateException("Summary jobs for this QScript are already executed")
     val writeSummary = new WriteSummary(this)
 
     def addChecksum(file: File): Unit = {
@@ -160,6 +163,8 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
         logger.info("Write summary is skipped because sample flag is used")
       case _ => add(writeSummary)
     }
+
+    addedJobs = true
   }
 }