Remove addAllJobs from CufflinksProducer

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

@@ -38,6 +38,9 @@ trait CufflinksProducer { this: Gentrap#Sample =>
       case otherwise       => throw new IllegalStateException("Unexpected cufflinks type: " + otherwise.toString)
     }
 
+    /** Container for all jobs in this job set */
+    def jobs = Seq(cufflinksJob, geneFpkmJob, isoformFpkmJob)
+
     /** The main cufflinks job */
     lazy val cufflinksJob: Cufflinks = {
       val job = new Cufflinks(pipeline) {
@@ -73,8 +76,5 @@ trait CufflinksProducer { this: Gentrap#Sample =>
       job.output = new File(cufflinksJob.output_dir, s"$sampleId.isoformss_fpkm_$name")
       job
     }
-
-    /** Adds all contained jobs to Queue */
-    def addAllJobs(): Unit = { pipeline.add(cufflinksJob); pipeline.add(geneFpkmJob); pipeline.add(isoformFpkmJob) }
   }
 }

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

@@ -691,9 +691,9 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
       basesPerExonJob.foreach(add(_))
       // symlink results with distinct extensions ~ actually to make it easier to use MergeTables on these as well
       // since the Queue argument parser doesn't play nice with Map[_, _] types
-      cufflinksStrictJobSet.foreach(_.addAllJobs())
-      cufflinksGuidedJobSet.foreach(_.addAllJobs())
-      cufflinksBlindJobSet.foreach(_.addAllJobs())
+      cufflinksStrictJobSet.foreach(_.jobs.foreach(add(_)))
+      cufflinksGuidedJobSet.foreach(_.jobs.foreach(add(_)))
+      cufflinksBlindJobSet.foreach(_.jobs.foreach(add(_)))
       // add variant calling job if requested
       varCallJob.foreach(add(_))
     }