Merge branch 'feature-full-fastq-to-gears' into 'develop'

Feature full fastq to gears

- Fixes BIOPET-398
- Fixes BIOPET-411
- Fixes BIOPET-414

See merge request !469

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

@@ -26,6 +26,50 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
   @Output(doc = "Output with hits per sequence")
   var report: Option[File] = None
 
+  @Output(required = false)
+  var un: Option[File] = None
+
+  @Output(required = false)
+  var al: Option[File] = None
+
+  @Output(required = false)
+  var unConc: Option[File] = None
+
+  @Output(required = false)
+  var alConc: Option[File] = None
+
+  @Output(required = false)
+  var metFile: Option[File] = None
+
+  // Input args
+  var q: Boolean = config("q", default = false)
+  var qseq: Boolean = config("qseq", default = false)
+  var f: Boolean = config("f", default = false)
+  var r: Boolean = config("r", default = false)
+  var c: Boolean = config("c", default = false)
+  var skip: Option[Int] = config("skip")
+  var upto: Option[Int] = config("upto")
+  var trim5: Option[Int] = config("trim5")
+  var trim3: Option[Int] = config("trim3")
+  var phred33: Boolean = config("phred33", default = false)
+  var phred64: Boolean = config("phred64", default = false)
+  var intQuals: Boolean = config("int_quals", default = false)
+  var ignoreQuals: Boolean = config("ignore_quals", default = false)
+  var nofw: Boolean = config("nofw", default = false)
+  var norc: Boolean = config("norc", default = false)
+
+  // Classification args
+  var minHitlen: Option[Int] = config("min_hitlen")
+  var minTotallen: Option[Int] = config("min_totallen")
+  var hostTaxids: List[Int] = config("host_taxids", default = Nil)
+  var excludeTaxids: List[Int] = config("exclude_taxids", default = Nil)
+
+  // Output args
+  var t: Boolean = config("t", default = false)
+  var quiet: Boolean = config("quiet", default = false)
+  var metStderr: Boolean = config("met_stderr", default = false)
+  var met: Option[Int] = config("met")
+
   override def defaultThreads = 8
 
   executable = config("exe", default = "centrifuge", freeVar = false)
@@ -49,7 +93,34 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
    * @return Command to run
    */
   def cmdLine: String = executable +
-    //TODO: Options
+    conditional(q, "-q") +
+    conditional(qseq, "--qseq") +
+    conditional(f, "-f") +
+    conditional(r, "-r") +
+    conditional(c, "-c") +
+    optional("--skip", skip) +
+    optional("--upto", upto) +
+    optional("--trim5", trim5) +
+    optional("--trim3", trim3) +
+    conditional(phred33, "--phred33") +
+    conditional(phred64, "--phred64") +
+    conditional(intQuals, "--int-quals") +
+    conditional(ignoreQuals, "--ignore-quals") +
+    conditional(nofw, "--nofw") +
+    conditional(norc, "--norc") +
+    optional("--min-hitlen", minHitlen) +
+    optional("--min-totallen", minTotallen) +
+    optional("--host-taxids", if (hostTaxids.nonEmpty) Some(hostTaxids.mkString(",")) else None) +
+    optional("--exclude-taxids", if (excludeTaxids.nonEmpty) Some(excludeTaxids.mkString(",")) else None) +
+    optional("--met-file", metFile) +
+    conditional(t, "-t") +
+    conditional(quiet, "--quiet") +
+    conditional(metStderr, "--met-stderr") +
+    optional("--met", met) +
+    optional(if (un.exists(_.getName.endsWith(".gz"))) "--un-gz" else "--un", un) +
+    optional(if (al.exists(_.getName.endsWith(".gz"))) "--al-gz" else "--al", al) +
+    optional(if (unConc.exists(_.getName.endsWith(".gz"))) "--un-conc-gz" else "--un-conc", unConc) +
+    optional(if (alConc.exists(_.getName.endsWith(".gz"))) "--al-conc-gz" else "--al-conc", alConc) +
     optional("--threads", threads) +
     required("-x", index) +
     (inputR2 match {

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

@@ -163,8 +163,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
           gs.libId = Some(libId)
           gs.outputDir = libDir
 
-          gs.fastqR1 = Some(addDownsample(flexiprep.fastqR1Qc, gs.outputDir))
-          gs.fastqR2 = flexiprep.fastqR2Qc.map(addDownsample(_, gs.outputDir))
+          gs.fastqR1 = List(addDownsample(flexiprep.fastqR1Qc, gs.outputDir))
+          gs.fastqR2 = flexiprep.fastqR2Qc.map(addDownsample(_, gs.outputDir)).toList
           add(gs)
         }
       }
@@ -194,8 +194,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
         add(Zcat(qscript, flexipreps.flatMap(_.fastqR2Qc)) | new Gzip(qscript) > file)
       }
 
-      gearsSingle.fastqR1 = Some(addDownsample(mergeR1, gearsSingle.outputDir))
-      gearsSingle.fastqR2 = mergeR2.map(addDownsample(_, gearsSingle.outputDir))
+      gearsSingle.fastqR1 = List(addDownsample(mergeR1, gearsSingle.outputDir))
+      gearsSingle.fastqR2 = mergeR2.map(addDownsample(_, gearsSingle.outputDir)).toList
       add(gearsSingle)
     }
 

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

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -29,10 +30,10 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   def this() = this(null)
 
   @Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
-  var fastqR1: Option[File] = None
+  var fastqR1: List[File] = Nil
 
   @Input(doc = "R2 reads in FastQ format", shortName = "R2", required = false)
-  var fastqR2: Option[File] = None
+  var fastqR2: List[File] = Nil
 
   @Input(doc = "All unmapped reads will be extracted from this bam for analysis", shortName = "bam", required = false)
   var bamFile: Option[File] = None
@@ -40,8 +41,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   @Argument(required = false)
   var outputName: String = _
 
-  lazy val krakenScript = if (config("gears_use_kraken", default = true)) Some(new GearsKraken(this)) else None
-  lazy val centrifugeScript = if (config("gears_use_centrifuge", default = false)) Some(new GearsCentrifuge(this)) else None
+  lazy val krakenScript = if (config("gears_use_kraken", default = false)) Some(new GearsKraken(this)) else None
+  lazy val centrifugeScript = if (config("gears_use_centrifuge", default = true)) Some(new GearsCentrifuge(this)) else None
   lazy val qiimeRatx = if (config("gears_use_qiime_rtax", default = false)) Some(new GearsQiimeRtax(this)) else None
   lazy val qiimeClosed = if (config("gears_use_qiime_closed", default = false)) Some(new GearsQiimeClosed(this)) else None
   lazy val qiimeOpen = if (config("gears_use_qiime_open", default = false)) Some(new GearsQiimeOpen(this)) else None
@@ -49,12 +50,13 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
 
   /** Executed before running the script */
   def init(): Unit = {
-    if (!fastqR1.isDefined && !bamFile.isDefined) Logging.addError("Please specify fastq-file(s) or bam file")
-    if (fastqR1.isDefined == bamFile.isDefined) Logging.addError("Provide either a bam file or a R1/R2 file")
+    if (fastqR1.isEmpty && !bamFile.isDefined) Logging.addError("Please specify fastq-file(s) or bam file")
+    if (fastqR1.nonEmpty == bamFile.isDefined) Logging.addError("Provide either a bam file or a R1/R2 file")
+    if (fastqR2.nonEmpty && fastqR1.size != fastqR2.size) Logging.addError("R1 and R2 has not the same number of files")
     if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on GearsSingle module")
 
     if (outputName == null) {
-      if (fastqR1.isDefined) outputName = fastqR1.map(_.getName
+      if (fastqR1.nonEmpty) outputName = fastqR1.headOption.map(_.getName
         .stripSuffix(".gz")
         .stripSuffix(".fastq")
         .stripSuffix(".fq"))
@@ -62,7 +64,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
       else outputName = bamFile.map(_.getName.stripSuffix(".bam")).getOrElse("noName")
     }
 
-    if (fastqR1.isDefined) {
+    if (fastqR1.nonEmpty) {
       fastqR1.foreach(inputFiles :+= InputFile(_))
       fastqR2.foreach(inputFiles :+= InputFile(_))
     } else bamFile.foreach(inputFiles :+= InputFile(_))
@@ -79,30 +81,42 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
 
   protected var skipFlexiprep: Boolean = config("skip_flexiprep", default = false)
 
-  protected def executeFlexiprep(r1: File, r2: Option[File]): (File, Option[File]) = {
+  protected def executeFlexiprep(r1: List[File], r2: List[File]): (File, Option[File]) = {
+    val read1: File = if (r1.size == 1) r1.head else {
+      val outputFile = new File(outputDir, "merged.R1.fq.gz")
+      Zcat(this, r1) | new Gzip(this) > outputFile
+      outputFile
+    }
+
+    val read2: Option[File] = if (r2.size <= 1) r2.headOption else {
+      val outputFile = new File(outputDir, "merged.R2.fq.gz")
+      Zcat(this, r2) | new Gzip(this) > outputFile
+      Some(outputFile)
+    }
+
     if (!skipFlexiprep) {
       val flexiprep = new Flexiprep(this)
-      flexiprep.inputR1 = r1
-      flexiprep.inputR2 = r2
+      flexiprep.inputR1 = read1
+      flexiprep.inputR2 = read2
       flexiprep.sampleId = if (sampleId.isEmpty) Some("noSampleName") else sampleId
       flexiprep.libId = if (libId.isEmpty) Some("noLibName") else libId
       flexiprep.outputDir = new File(outputDir, "flexiprep")
       add(flexiprep)
       (flexiprep.fastqR1Qc, flexiprep.fastqR2Qc)
-    } else (r1, r2)
+    } else (read1, read2)
   }
 
   /** Method to add jobs */
   def biopetScript(): Unit = {
     val (r1, r2): (File, Option[File]) = (fastqR1, fastqR2, bamFile) match {
-      case (Some(r1), _, _) => executeFlexiprep(r1, fastqR2)
+      case (r1, _, _) if r1.nonEmpty => executeFlexiprep(r1, fastqR2)
       case (_, _, Some(bam)) =>
         val extract = new ExtractUnmappedReads(this)
         extract.outputDir = outputDir
         extract.bamFile = bam
         extract.outputName = outputName
         add(extract)
-        executeFlexiprep(extract.fastqUnmappedR1, extract.fastqUnmappedR2)
+        executeFlexiprep(extract.fastqUnmappedR1 :: Nil, extract.fastqUnmappedR2.toList)
       case _ => throw new IllegalArgumentException("Missing input files")
     }
 
@@ -178,8 +192,8 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   /** Statistics shown in the summary file */
   def summaryFiles: Map[String, File] = Map.empty ++
     (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
-    (if (fastqR1.isDefined) Map("input_R1" -> fastqR1.get) else Map()) ++
-    (if (fastqR2.isDefined) Map("input_R2" -> fastqR2.get) else Map()) ++
+    fastqR1.zipWithIndex.map(x => s"input_R1_${x._2}" -> x._1) ++
+    fastqR2.zipWithIndex.map(x => s"input_R2_${x._2}" -> x._1) ++
     outputFiles
 }
 

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

@@ -23,23 +23,26 @@ class GearsSingleReport(val root: Configurable) extends ReportBuilderExtension {
 
 object GearsSingleReport extends ReportBuilder {
 
-  // TODO: Add dustbin analysis (aggregated)
-  // TODO: Add alignment stats per sample for the dustbin analysis
-
   override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
     .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
 
   def indexPage = {
+    val krakenExecuted = summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").isDefined
+    val centrifugeExecuted = summary.getValue(sampleId, libId, "gearscentrifuge", "stats", "centrifuge_report").isDefined
+
     ReportPage(
       List(
-        "Versions" -> ReportPage(List(), List((
-          "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
-          ))), Map())
-      ),
-      List(
-        "Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"),
-        "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")
+        "Versions" -> ReportPage(List(),
+          List(("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"))), Map())
       ),
+      List("Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp")) ++
+        (if (krakenExecuted) List("Kraken analysis" ->
+          ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"))
+        else Nil) ++
+        (if (centrifugeExecuted) List("Centrifuge analysis" ->
+          ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+            Map("summaryModuleTag" -> "gearscentrifuge", "summaryStatsTag" -> "centrifuge_unique_report")))
+        else Nil),
       pageArgs
     )
   }

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

@@ -80,8 +80,8 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
 
     inputMode match {
       case Some("fastq") =>
-        gears.fastqR1 = Some(TestGearsSingle.r1)
-        gears.fastqR2 = if (paired) Some(TestGearsSingle.r2) else None
+        gears.fastqR1 = List(TestGearsSingle.r1)
+        gears.fastqR2 = if (paired) List(TestGearsSingle.r2) else Nil
       case Some("bam") => gears.bamFile = Some(TestGearsSingle.bam)
       case None        =>
       case _           => new IllegalStateException(s"$inputMode not allowed as inputMode")
@@ -108,12 +108,12 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
 
       val pipesJobs = gears.functions.filter(_.isInstanceOf[BiopetPipe]).flatMap(_.asInstanceOf[BiopetPipe].pipesJobs)
 
-      gears.summarySettings("gears_use_kraken") shouldBe kraken.getOrElse(true)
+      gears.summarySettings("gears_use_kraken") shouldBe kraken.getOrElse(false)
       gears.summarySettings("gear_use_qiime_rtax") shouldBe qiimeRtax
       gears.summarySettings("gear_use_qiime_closed") shouldBe qiimeClosed
       gears.summarySettings("gear_use_qiime_open") shouldBe qiimeOpen
 
-      gears.krakenScript.isDefined shouldBe kraken.getOrElse(true)
+      gears.krakenScript.isDefined shouldBe kraken.getOrElse(false)
       gears.centrifugeScript.isDefined shouldBe centrifuge
       gears.qiimeClosed.isDefined shouldBe qiimeClosed
       gears.qiimeOpen.isDefined shouldBe qiimeOpen
@@ -124,10 +124,10 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
       gears.functions.count(_.isInstanceOf[SamtoolsView]) shouldBe (if (inputMode == Some("bam")) 1 else 0)
       gears.functions.count(_.isInstanceOf[SamToFastq]) shouldBe (if (inputMode == Some("bam")) 1 else 0)
 
-      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[Kraken]) shouldBe (if (kraken.getOrElse(false)) 1 else 0)
+      gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe (if (kraken.getOrElse(false)) 1 else 0)
       gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe
-        ((if (kraken.getOrElse(true)) 1 else 0) + (if (centrifuge) 2 else 0))
+        ((if (kraken.getOrElse(false)) 1 else 0) + (if (centrifuge) 2 else 0))
 
       gears.functions.count(_.isInstanceOf[Centrifuge]) shouldBe (if (centrifuge) 1 else 0)
       gears.functions.count(_.isInstanceOf[CentrifugeKreport]) shouldBe (if (centrifuge) 2 else 0)

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

@@ -130,7 +130,10 @@ object GearsTest {
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),
     "cutadapt" -> Map("exe" -> "test"),
-    "pickopenreferenceotus" -> Map("exe" -> "test")
+    "centrifuge" -> Map("exe" -> "test"),
+    "centrifuge_index" -> "test",
+    "pickopenreferenceotus" -> Map("exe" -> "test"),
+    "centrifugekreport" -> Map("exe" -> "test")
   )
 
   val sample1 = Map(

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala

@@ -218,6 +218,14 @@ trait MultisampleMappingTrait extends MultiSampleQScript
     /** Default is set to keep the merged files, user can set this in the config. To change the default this method can be overriden */
     def keepMergedFiles: Boolean = config("keep_merged_files", default = true)
 
+    /**
+     * @deprecated
+     */
+    lazy val unmappedToGears: Boolean = config("unmapped_to_gears", default = false)
+    if (config.contains("unmapped_to_gears")) logger.warn("Config value 'unmapped_to_gears' is replaced with 'mapping_to_gears', Assumes default: mapping_to_gears=unmapped")
+
+    lazy val mappingToGears: String = config("mapping_to_gears", default = if (unmappedToGears) "unmapped" else "none")
+
     /** This method can be extended to add jobs to the pipeline, to do this the super call of this function must be called by the pipelines */
     def addJobs(): Unit = {
       addPerLibJobs() // This add jobs for each library
@@ -249,12 +257,22 @@ trait MultisampleMappingTrait extends MultiSampleQScript
         if (config("execute_bam2wig", default = true)) add(Bam2Wig(qscript, preProcessBam.get))
       }
 
-      if (config("unmapped_to_gears", default = false) && libraries.flatMap(_._2.bamFile).nonEmpty) {
-        val gears = new GearsSingle(qscript)
-        gears.bamFile = preProcessBam
-        gears.sampleId = Some(sampleId)
-        gears.outputDir = new File(sampleDir, "gears")
-        add(gears)
+      mappingToGears match {
+        case "unmapped" =>
+          val gears = new GearsSingle(qscript)
+          gears.bamFile = preProcessBam
+          gears.sampleId = Some(sampleId)
+          gears.outputDir = new File(sampleDir, "gears")
+          add(gears)
+        case "all" =>
+          val gears = new GearsSingle(qscript)
+          gears.fastqR1 = libraries.flatMap(_._2.inputR1).toList
+          gears.fastqR2 = libraries.flatMap(_._2.inputR2).toList
+          gears.sampleId = Some(sampleId)
+          gears.outputDir = new File(sampleDir, "gears")
+          add(gears)
+        case "none" =>
+        case x      => Logging.addError(s"${x} is not a valid value for 'mapping_to_gears'")
       }
     }
   }

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -14,9 +14,10 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
 import nl.lumc.sasc.biopet.extensions.kraken.Kraken
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
 import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -25,7 +26,7 @@ import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ AfterClass, BeforeClass, DataProvider, Test }
+import org.testng.annotations.{AfterClass, BeforeClass, DataProvider, Test}
 
 /**
  * Test class for [[Mapping]]
@@ -88,7 +89,7 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     //Flexiprep
     mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
 
-    mapping.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (unmappedToGears) 1 else 0)
+    mapping.functions.count(_.isInstanceOf[Centrifuge]) shouldBe (if (unmappedToGears) 1 else 0)
   }
 
   val outputDir = Files.createTempDir()
@@ -143,6 +144,9 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     "samtools" -> Map("exe" -> "test"),
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "krakenreport" -> Map("exe" -> "test", "db" -> "test"),
+    "centrifuge" -> Map("exe" -> "test"),
+    "centrifugekreport" -> Map("exe" -> "test"),
+    "centrifuge_index" -> "test",
     "md5sum" -> Map("exe" -> "test")
   )
 

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -14,17 +14,18 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
+import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
 import nl.lumc.sasc.biopet.extensions.kraken.Kraken
-import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
-import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
+import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles}
+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
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
+import org.testng.annotations.{DataProvider, Test}
 
 /**
  * Created by pjvanthof on 15/05/16.
@@ -102,7 +103,7 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
           }
       }
 
-      pipeline.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (unmappedToGears) (numberFastqLibs + numberSamples) else 0)
+      pipeline.functions.count(_.isInstanceOf[Centrifuge]) shouldBe (if (unmappedToGears) (numberFastqLibs + numberSamples) else 0)
 
       pipeline.summarySettings.get("merge_strategy") shouldBe Some(merge.toString)
     }
@@ -198,6 +199,9 @@ object MultisampleMappingTestTrait {
     "wigtobigwig" -> Map("exe" -> "test"),
     "kraken" -> Map("exe" -> "test", "db" -> "test"),
     "krakenreport" -> Map("exe" -> "test", "db" -> "test"),
+    "centrifuge" -> Map("exe" -> "test"),
+    "centrifugekreport" -> Map("exe" -> "test"),
+    "centrifuge_index" -> "test",
     "md5sum" -> Map("exe" -> "test")
   )