Fix bug when bowtie2 is not able to find reference files ending with .bt2l...

Fix bug when bowtie2 is not able to find reference files ending with .bt2l (new large file definition)

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala

@@ -135,7 +135,12 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
     val indexDir = new File(bowtieIndex).getParentFile
     val basename = bowtieIndex.stripPrefix(indexDir.getPath + File.separator)
     if (indexDir.exists()) {
-      if (!indexDir.list().toList.filter(_.startsWith(basename)).exists(_.endsWith(".bt2")))
+      if (!indexDir.list()
+        .toList
+        .filter(_.startsWith(basename))
+        .exists({ p =>
+          p.endsWith(".bt2") || p.endsWith(".bt2l")
+        }))
         Logging.addError(s"No index files found for bowtie2 in: $indexDir with basename: $basename")
     }
   }