Fix output path for pindel (pindel outputs to certain dir with prefix_)

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala

@@ -123,6 +123,9 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
       }
     }
 
+    // modify `output_prefix` to include samplename
+    output_prefix = new File(output_prefix + File.separator,  "sample" )
+
     // set the output file
     output_file = new File(output_prefix, "_D")
   }