Fix type

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala

@@ -35,11 +35,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
     means we have 2 samples, each with 2 replicates
     so our input is a list of lists of Files
    */
-  var input: List[List[File]] = List.empty[List[File]]
+  var input: List[List[File]] = Nil
 
   /** input GTF file */
   @Input(doc = "Input GTF file", required = true)
-  var transcriptsGtf: File = null
+  var transcriptsGtf: File = _
 
   /** output file, computed automatically from output directory */
   @Output(doc = "Output CXB file")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala

@@ -38,9 +38,9 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()
-    deps :+= index + ".1.cf"
-    deps :+= index + ".2.cf"
-    deps :+= index + ".3.cf"
+    deps :+= new File(index + ".1.cf")
+    deps :+= new File(index + ".2.cf")
+    deps :+= new File(index + ".3.cf")
   }
 
   /**

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala

@@ -31,9 +31,9 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
 
   override def beforeGraph(): Unit = {
     super.beforeGraph()
-    deps :+= index + ".1.cf"
-    deps :+= index + ".2.cf"
-    deps :+= index + ".3.cf"
+    deps :+= new File(index + ".1.cf")
+    deps :+= new File(index + ".2.cf")
+    deps :+= new File(index + ".3.cf")
   }
 
   def cmdLine = executable +