Major upgrade to gentrap class

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala

@@ -36,9 +36,11 @@ trait AnnotationRefFlat extends BiopetQScript { qscript: QScript =>
 
 trait RibosomalRefFlat extends BiopetQScript { qscript: QScript =>
   /** GTF reference file */
-  lazy val ribosomalRefFlat: File = {
-    val file: File = config("ribosome_refflat", freeVar = true)
-    inputFiles :+ InputFile(file, config("ribosome_refflat_md5", freeVar = true))
+  lazy val ribosomalRefFlat: Option[File] = {
+    val file: Option[File] = config("ribosome_refflat", freeVar = true)
+    file match {
+      case Some(f) => inputFiles :+ InputFile(f, config("ribosome_refflat_md5", freeVar = true))
+    }
     file
   }
 }

public/gentrap/pom.xml

@@ -33,6 +33,11 @@
     <name>Gentrap</name>
 
     <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Shiva</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Mapping</artifactId>