No merging with only 1 sample

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -80,7 +80,7 @@ class Star(val parent: Configurable)
   var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases")
   var genomeSAsparseD: Option[Int] = config("genomesasparsed")
 
-  val defaultGtf: Option[File] = config("annotation_gtf")
+  private def defaultGtf: Option[File] = config("annotation_gtf")
   @Input(required = false)
   var sjdbGTFfile: Option[File] = defaultGtf match {
     case Some(file) => config("sjdbgtfile", default = file)

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala

@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
     require(bamFiles.nonEmpty)
   }
 
-  lazy val mergeCountFiles: Boolean = config("merge_count_files", default = true)
+  lazy val mergeCountFiles: Boolean = config("merge_count_files", default = bamFiles.size > 1)
 
   private var extraSummaryFiles: Map[String, File] = Map()