fai and dict check are not optional

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

@@ -37,10 +37,14 @@ trait Reference extends Configurable {
     List("references", referenceSpecies, referenceName)
   }
 
+  protected def faiRequired = false
+
+  protected def dictRequired = false
+
   /** Returns the fasta file */
   def referenceFasta(): File = {
     val file: File = config("reference_fasta")
-    Reference.checkFasta(file)
+    checkFasta(file)
 
     val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
     val fai = new File(file.getAbsolutePath + ".fai")
@@ -65,29 +69,32 @@ trait Reference extends Configurable {
       "name" -> referenceName
     )
   }
-}
-
-object Reference {
-
-  /** Used as cache to avoid double checking */
-  private var checked: Set[File] = Set()
 
   //TODO: this become obsolete when index get autogenerated
 
   /** Check fasta file if file exist and index file are there */
   def checkFasta(file: File): Unit = {
-    if (!checked.contains(file)) {
+    if (!Reference.checked.contains(file)) {
       require(file.exists(), "Reference not found: " + file)
 
-      val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
-      require(dict.exists(), "Reference is missing a dict file")
-
-      val fai = new File(file.getAbsolutePath + ".fai")
-      require(fai.exists(), "Reference is missing a fai file")
+      if (dictRequired) {
+        val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+        require(dict.exists(), "Reference is missing a dict file")
+      }
 
-      require(IndexedFastaSequenceFile.canCreateIndexedFastaReader(file), "Index of reference cannot be loaded, reference: " + file)
+      if (faiRequired) {
+        val fai = new File(file.getAbsolutePath + ".fai")
+        require(fai.exists(), "Reference is missing a fai file")
+        require(IndexedFastaSequenceFile.canCreateIndexedFastaReader(file), "Index of reference cannot be loaded, reference: " + file)
+      }
 
-      checked += file
+      Reference.checked += file
     }
   }
 }
+
+object Reference {
+
+  /** Used as cache to avoid double checking */
+  private var checked: Set[File] = Set()
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

@@ -48,6 +48,8 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
   @Input(required = false)
   var pedigree: List[File] = config("pedigree", default = Nil)
 
+  override def dictRequired = true
+
   override def beforeGraph: Unit = {
     super.beforeGraph
     if (reference == null) reference = referenceFasta()