Fixed output of centrifuge

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import nl.lumc.sasc.biopet.core.SampleLibraryTag
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.Gzip
-import nl.lumc.sasc.biopet.extensions.centrifuge.{Centrifuge, CentrifugeKreport}
+import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
 import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
@@ -27,18 +27,21 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     require(outputName != null)
   }
 
+  def centrifugeOutput = new File(outputDir, s"$outputName.centrifuge.gz")
+
   def biopetScript(): Unit = {
-    val centrifugeOutput = new File(outputDir, s"$outputName.centrifuge.gz")
     val centrifuge = new Centrifuge(this)
     centrifuge.inputR1 = fastqR1
     centrifuge.inputR2 = fastqR2
+    centrifuge.output = new File(outputDir, s"$outputName.centrifuge")
     centrifuge.report = Some(new File(outputDir, s"$outputName.centrifuge.report"))
-    val cmd = centrifuge | new Gzip(this) > centrifugeOutput
-    cmd.threadsCorrection = -1
-    add(cmd)
+    centrifuge.isIntermediate = true
+    add(centrifuge)
+
+    add(centrifuge.output :<: new Gzip(this) > centrifugeOutput)
 
-    makeKreport(List(centrifugeOutput), "centrifuge", unique = false)
-    makeKreport(List(centrifugeOutput), "centrifuge_unique", unique = true)
+    makeKreport(List(centrifuge.output), "centrifuge", unique = false)
+    makeKreport(List(centrifuge.output), "centrifuge_unique", unique = true)
 
     addSummaryJobs()
   }
@@ -65,9 +68,10 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
   def summarySettings: Map[String, Any] = Map()
 
   /** Statistics shown in the summary file */
-  def summaryFiles: Map[String, File] = outputFiles + ("input_R1" -> fastqR1) ++ (fastqR2 match {
-    case Some(file) => Map("input_R2" -> file)
-    case _          => Map()
-  })
+  def summaryFiles: Map[String, File] = outputFiles + ("input_R1" -> fastqR1, "centrifuge_output" -> centrifugeOutput) ++
+    (fastqR2 match {
+      case Some(file) => Map("input_R2" -> file)
+      case _          => Map()
+    })
 
 }

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

@@ -18,12 +18,12 @@ import java.io.File
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.BiopetPipe
-import nl.lumc.sasc.biopet.extensions.centrifuge.{Centrifuge, CentrifugeKreport}
-import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
+import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
+import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
 import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers