Added executables to testing

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

@@ -19,7 +19,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
   var inputR2: Option[File] = None
 
   @Input(doc = "Centrifuge index prefix", required = true)
-  var index: File = config("centrifige_index")
+  var index: File = config("centrifuge_index")
 
   @Output(doc = "Output with hits per sequence")
   var output: File = _

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

@@ -17,7 +17,7 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
   var output: File = _
 
   @Input(doc = "Centrifuge index prefix", required = true)
-  var index: File = config("centrifige_index", namespace = "centrifuge")
+  var index: File = config("centrifuge_index", namespace = "centrifuge")
 
   executable = config("exe", default = "centrifuge-kreport", freeVar = false)
 

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -231,6 +231,8 @@ object TestGearsSingle {
 
   val executables = Map(
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
+    "centrifuge" -> Map("exe" -> "test", "centrifuge_index" -> "test"),
+    "centrifugekreport" -> Map("exe" -> "test"),
     "krakenreport" -> Map("exe" -> "test", "db" -> "test"),
     "sambamba" -> Map("exe" -> "test"),
     "samtools" -> Map("exe" -> "test"),