forcing the user to set the 'maxins' parameter

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala

@@ -74,6 +74,9 @@ class Bowtie(val parent: Configurable)
             s"No index files found for bowtie in: $indexDir with basename: $basename")
       }
     }
+    if (R2.nonEmpty && maxins.isEmpty) {
+      Logging.addError("The parameter 'maxins' that specifies the maximum allowed insert size, is missing in the configuration. Please note that Bowtie won't align reads coming from inserts longer than this value.")
+    }
   }
 
   /** return commandline to execute */