Fixing output dir

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

@@ -120,7 +120,11 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
 
   private def createRun(): Int = {
     val db = SummaryDb.openSqliteSummary(summaryDbFile)
-    val id = Await.result(db.createRun(summaryName, outputDir), Duration.Inf)
+    val dir = root match {
+      case q:BiopetQScript => q.outputDir
+      case _ => throw new IllegalStateException("Root should be a BiopetQscript")
+    }
+    val id = Await.result(db.createRun(summaryName, dir.getAbsolutePath), Duration.Inf)
     runIdFile.getParentFile.mkdir()
     val writer = new PrintWriter(runIdFile)
     writer.println(id)