Adding centrifuge to testing

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

@@ -9,8 +9,8 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.util.matching.Regex
 
 /**
-  * Created by pjvanthof on 19/09/16.
-  */
+ * Created by pjvanthof on 19/09/16.
+ */
 class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with Version {
   @Input(doc = "Input: FastQ or FastA", required = true)
   var inputR1: File = _
@@ -38,14 +38,14 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
   def versionRegex: Regex = ".* version (.*)".r
 
   /**
-    * This function needs to be implemented to define the command that is executed
-    *
-    * @return Command to run
-    */
+   * This function needs to be implemented to define the command that is executed
+   *
+   * @return Command to run
+   */
   def cmdLine: String = executable +
     //TODO: Options
     optional("--threads", threads)
-    required("-x", index) +
+  required("-x", index) +
     (inputR2 match {
       case Some(r2) => required("-1", inputR1) + required("-2", r2)
       case _        => required("-U", inputR1)

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

@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
-  * Created by pjvanthof on 19/09/16.
-  */
+ * 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

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

@@ -8,8 +8,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /**
-  * Created by pjvanthof on 19/09/16.
-  */
+ * Created by pjvanthof on 19/09/16.
+ */
 class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
 
   var fastqR1: File = _
@@ -35,7 +35,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
     add(centrifuge)
 
     val centrifugeKreport = new CentrifugeKreport(this)
-    centrifugeKreport.centrifugeOutputFiles += centrifuge.output
+    centrifugeKreport.centrifugeOutputFiles :+= centrifuge.output
     centrifugeKreport.output = new File(outputDir, s"$outputName.centrifuge.kreport")
     add(centrifugeKreport)
 

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

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import java.io.File
 
 import com.google.common.io.Files
+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
@@ -49,6 +50,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
   def paired: Boolean = false
   def hasOutputName: Boolean = false
   def kraken: Option[Boolean] = None
+  def centrifuge: Boolean = false
   def qiimeClosed: Boolean = false
   def qiimeOpen: Boolean = false
   def qiimeRtax: Boolean = false
@@ -61,6 +63,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
   def testGears(): Unit = {
     val map = ConfigUtils.mergeMaps(Map(
       "gears_use_qiime_rtax" -> qiimeRtax,
+      "gears_use_centrifuge" -> centrifuge,
       "gears_use_qiime_closed" -> qiimeClosed,
       "gears_use_qiime_open" -> qiimeOpen,
       "gears_use_seq_count" -> seqCount,
@@ -108,6 +111,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
       gears.summarySettings("gear_use_qiime_open") shouldBe qiimeOpen
 
       gears.krakenScript.isDefined shouldBe kraken.getOrElse(true)
+      gears.centrifugeScript.isDefined shouldBe centrifuge
       gears.qiimeClosed.isDefined shouldBe qiimeClosed
       gears.qiimeOpen.isDefined shouldBe qiimeOpen
       gears.qiimeRatx.isDefined shouldBe qiimeRtax
@@ -119,7 +123,11 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
 
       gears.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
       gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
-      gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
+      gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe
+        ((if (kraken.getOrElse(true)) 1 else 0) + (if (centrifuge) 1 else 0))
+
+      gears.functions.count(_.isInstanceOf[Centrifuge]) shouldBe (if (centrifuge) 1 else 0)
+      gears.functions.count(_.isInstanceOf[CentrifugeKreport]) shouldBe (if (centrifuge) 1 else 0)
     }
   }
 }
@@ -132,6 +140,9 @@ class GearsSingleDefaultTest extends TestGearsSingle
 class GearsSingleKrakenTest extends TestGearsSingle {
   override def kraken = Some(true)
 }
+class GearsSingleCentrifugeTest extends TestGearsSingle {
+  override def centrifuge = true
+}
 class GearsSingleQiimeClosedTest extends TestGearsSingle {
   override def qiimeClosed = true
 }
@@ -149,6 +160,10 @@ class GearsSingleKrakenPairedTest extends TestGearsSingle {
   override def paired = true
   override def kraken = Some(true)
 }
+class GearsSingleCentrifugePairedTest extends TestGearsSingle {
+  override def paired = true
+  override def centrifuge = true
+}
 class GearsSingleQiimeClosedPairedTest extends TestGearsSingle {
   override def paired = true
   override def qiimeClosed = true
@@ -168,6 +183,7 @@ class GearsSingleseqCountPairedTest extends TestGearsSingle {
 
 class GearsSingleAllTest extends TestGearsSingle {
   override def kraken = Some(true)
+  override def centrifuge = true
   override def qiimeClosed = true
   override def qiimeOpen = true
   override def qiimeRtax = true
@@ -175,6 +191,7 @@ class GearsSingleAllTest extends TestGearsSingle {
 }
 class GearsSingleAllPairedTest extends TestGearsSingle {
   override def kraken = Some(true)
+  override def centrifuge = true
   override def qiimeClosed = true
   override def qiimeOpen = true
   override def qiimeRtax = true