Update Gentrap dict test to be more test-friendly

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -306,14 +306,19 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
     job
   }
 
+  // used to ensure that the required .dict file is present before the run starts
+  // can not store it in config since the tools that use it (Picard) have this value based on the reference file name
+  protected def checkDictFile(): Unit = {
+    val refFile: File = config("reference")
+    val refName: String = refFile.getName
+    require(refName.contains('.'), "Reference file must have an extension")
+    val dictFile = new File(refName.take(refName.lastIndexOf('.')) + ".dict")
+    require(dictFile.exists, s"Dict file '$dictFile' must exist")
+  }
+
   /** Steps to run before biopetScript */
   def init(): Unit = {
-    // TODO: refactor this out to a submodule (mapping / bammetrics?)
-    // We require the reference FASTA to be present, and also its companion DICT file
-    require(config.contains("reference"), "Reference FASTA must be defined")
-    val refName: File = config("reference")
-    val dict: File = new File(refName.toString.take(refName.toString.lastIndexOf('.')) + ".dict")
-    require(dict.exists, s"Dict file '$dict' must exist")
+    checkDictFile()
 
     // TODO: validate that exons are flattened or not (depending on another option flag?)
     // validate required annotation files

public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -38,9 +38,10 @@ class GentrapTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Gentrap = {
     new Gentrap() {
       override def configName = "gentrap"
-
       override def globalConfig = new Config(map)
-
+      // disable dict file check since it is based on the reference file name (which we can't modify here since
+      // we use the mock /usr/bin/test file
+      override def checkDictFile: Unit = {}
       qSettings = new QSettings
       qSettings.runName = "test"
     }
@@ -187,6 +188,7 @@ object GentrapTest {
 
   val executables = Map(
     "reference" -> "test",
+    "dict" -> "test",
     "annotation_gtf" -> "test",
     "annotation_bed" -> "test",
     "annotation_refflat" -> "test",