Fixed input files

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

@@ -18,7 +18,6 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
   @Input(doc = "Input: FastQ or FastA", required = false)
   var inputR2: Option[File] = None
 
-  @Input(doc = "Centrifuge index prefix", required = true)
   var index: File = config("centrifuge_index")
 
   @Output(doc = "Output with hits per sequence")
@@ -37,6 +36,13 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
   /** Regex to get version from version command output */
   def versionRegex: Regex = ".* version (.*)".r
 
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    deps :+= index + ".1.cf"
+    deps :+= index + ".2.cf"
+    deps :+= index + ".3.cf"
+  }
+
   /**
    * This function needs to be implemented to define the command that is executed
    *

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

@@ -16,7 +16,6 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
   @Output(doc = "Output report")
   var output: File = _
 
-  @Input(doc = "Centrifuge index prefix", required = true)
   var index: File = config("centrifuge_index", namespace = "centrifuge")
 
   var onlyUnique: Boolean = config("only_unique", default = false)
@@ -30,6 +29,13 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
 
   executable = config("exe", default = "centrifuge-kreport", freeVar = false)
 
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    deps :+= index + ".1.cf"
+    deps :+= index + ".2.cf"
+    deps :+= index + ".3.cf"
+  }
+
   def cmdLine = executable +
     conditional(onlyUnique, "--only-unique") +
     conditional(showZeros, "--show-zeros") +