NO more reflective issues, simplify some refs.

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala

@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.tools.FastqSync
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.function.QFunction
 import scala.collection.JavaConversions._
-
+//import scala.language.reflectiveCalls
 /**
  * This is a trait for the Gears pipeline
  * The ShivaTrait is used as template for this pipeline
@@ -236,39 +236,41 @@ trait GearsTrait extends MultiSampleQScript with SummaryQScript { qscript =>
         case _               => None
       }
     }).flatten.toList)
-    lazy val alnFileDirty: File = sampleAlnJob.output
-    lazy val alnFile: File = sampleAlnJob.output
+    def alnFile: File = sampleBamLinkJob.output
 
     /** Job for combining all library BAMs */
-    private def sampleAlnJob: CombineFileFunction =
+    private def sampleBamLinkJob: Ln =
       makeCombineJob(libraries.values.map(_.alnFile).toList, createFile(".bam"))
 
-    /** Super type of Ln and MergeSamFiles */
-    private type CombineFileFunction = QFunction { def output: File }
-
     /** Ln or MergeSamFile job, depending on how many inputs are supplied */
     private def makeCombineJob(inFiles: List[File], outFile: File,
-                               mergeSortOrder: String = "coordinate"): CombineFileFunction = {
+                               mergeSortOrder: String = "coordinate"): Ln = {
       require(inFiles.nonEmpty, "At least one input files for combine job")
+      var input: File = new File("")
+
       if (inFiles.size == 1) {
-        val job = new Ln(qscript)
-        job.input = inFiles.head
-        job.output = outFile
-        job
+        input = inFiles.head
       } else {
+        val mergedBam = createFile(".merged.bam")
         val job = new MergeSamFiles(qscript)
         job.input = inFiles
-        job.output = outFile
+        job.output = mergedBam
         job.sortOrder = mergeSortOrder
-        job
+        input = job.output
       }
+
+      val job = new Ln(qscript)
+      job.input = input
+      job.output = outFile
+      job
+
     }
 
     /** This will add sample jobs */
     def addJobs(): Unit = {
       addPerLibJobs()
       // merge or symlink per-library alignments
-      add(sampleAlnJob)
+      add(sampleBamLinkJob)
 
       if (preProcessBam.isDefined) {
         val bamMetrics = new BamMetrics(qscript)