Added base version of centrifuge-kreport extension

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 = _
+  var index: File = config("centrifige_index")
 
   @Output(doc = "Output with hits per sequence")
   var output: File = _
@@ -42,7 +42,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
     *
     * @return Command to run
     */
-  protected[core] def cmdLine: String = executable +
+  def cmdLine: String = executable +
     //TODO: Options
     optional("--threads", threads)
     required("-x", index) +

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

+package nl.lumc.sasc.biopet.extensions.centrifuge
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+/**
+  * Created by pjvanthof on 19/09/16.
+  */
+class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunction {
+  @Input(doc = "Output files centrifuge", required = true)
+  var centrifugeOutputFiles: List[File] = Nil
+
+  @Output(doc = "Output report")
+  var output: File = _
+
+  @Input(doc = "Centrifuge index prefix", required = true)
+  var index: File = config("centrifige_index", namespace = "centrifuge")
+
+  executable = config("exe", default = "centrifuge-kreport", freeVar = false)
+
+  def cmdLine = executable +
+    //TODO: Options
+    required("-x", index) +
+    repeat(centrifugeOutputFiles)
+}