Removing the cd commands inside the job

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

@@ -54,7 +54,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     }
     writer.println("set -eubf")
     writer.println("set -o pipefail")
-    lines.foreach(writer.println)
+    //lines.foreach(writer.println)
+    writer.println(this.commandLine)
     jobDelayTime.foreach(x => writer.println(s"sleep $x"))
     writer.close()
   }
@@ -99,6 +100,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     beforeGraph()
     internalBeforeGraph()
 
+    this.commandDirectory = this.jobOutputFile.getParentFile
+
     super.freezeFieldValues()
   }