Change back to get

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

@@ -24,6 +24,9 @@ import org.broadinstitute.gatk.utils.commandline.Argument
  * @author Peter van 't Hof
  */
 trait SampleLibraryTag extends Configurable {
+
+  //FIXME: not possible to have required sample / lib
+
   @Argument(doc = "Sample ID", shortName = "sample", required = false)
   var sampleId: Option[String] = root match {
     case tag: SampleLibraryTag => tag.sampleId

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -442,10 +442,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
   def addBowtie2(R1: File, R2: Option[File], output: File): File = {
     val bowtie2 = new Bowtie2(this)
     bowtie2.rg_id = Some(readgroupId)
-    bowtie2.rg +:= ("LB:" + libId.getOrElse("x"))
+    bowtie2.rg +:= ("LB:" + libId.get)
     bowtie2.rg +:= ("PL:" + platform)
     bowtie2.rg +:= ("PU:" + platformUnit)
-    bowtie2.rg +:= ("SM:" + sampleId.getOrElse("x"))
+    bowtie2.rg +:= ("SM:" + sampleId.get)
     bowtie2.R1 = R1
     bowtie2.R2 = R2
     val sortSam = new SortSam(this)