Fixing job script

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -54,7 +54,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     }
     writer.println("set -eubf")
     writer.println("set -o pipefail")
-    writer.println(this.commandLine)
+    writer.println(lines.mkString("\n"))
     jobDelayTime.foreach(x => writer.println(s"sleep $x"))
     writer.close()
   }

gatk @ 677d7574

-Subproject commit a30ff57a56bee919a619190d43f22d3b8f9ef8d7
+Subproject commit 677d757419f515779766b10149b0e92eff71e5b2