Merge branch 'develop' into add-cnmops-kopisu

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala

@@ -35,11 +35,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
     means we have 2 samples, each with 2 replicates
     so our input is a list of lists of Files
    */
-  var input: List[List[File]] = List.empty[List[File]]
+  var input: List[List[File]] = Nil
 
   /** input GTF file */
   @Input(doc = "Input GTF file", required = true)
-  var transcriptsGtf: File = null
+  var transcriptsGtf: File = _
 
   /** output file, computed automatically from output directory */
   @Output(doc = "Output CXB file")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

@@ -40,6 +40,8 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction with Versio
 object Gzip {
   def apply(root: Configurable): Gzip = new Gzip(root)
 
+  def apply(root: Configurable, input: File, output: File): Gzip = Gzip(root, List(input), output)
+
   def apply(root: Configurable, input: List[File], output: File): Gzip = {
     val gzip = new Gzip(root)
     gzip.input = input

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

+package nl.lumc.sasc.biopet.extensions.centrifuge
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.util.matching.Regex
+
+/**
+ * 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 = _
+
+  @Input(doc = "Input: FastQ or FastA", required = false)
+  var inputR2: Option[File] = None
+
+  var index: File = config("centrifuge_index")
+
+  @Output(doc = "Output with hits per sequence")
+  var output: File = _
+
+  @Output(doc = "Output with hits per sequence")
+  var report: Option[File] = None
+
+  override def defaultThreads = 8
+
+  executable = config("exe", default = "centrifuge", freeVar = false)
+
+  /** Command to get version of executable */
+  def versionCommand: String = s"$executable --version"
+
+  /** Regex to get version from version command output */
+  def versionRegex: Regex = ".* version (.*)".r
+
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    deps :+= new File(index + ".1.cf")
+    deps :+= new File(index + ".2.cf")
+    deps :+= new File(index + ".3.cf")
+  }
+
+  /**
+   * 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) +
+    (inputR2 match {
+      case Some(r2) => required("-1", inputR1) + required("-2", r2)
+      case _        => required("-U", inputR1)
+    }) +
+    (if (outputAsStsout) "" else required("-S", output)) +
+    optional("--report-file", report)
+}

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 = _
+
+  var index: File = config("centrifuge_index", namespace = "centrifuge")
+
+  var onlyUnique: Boolean = config("only_unique", default = false)
+  var showZeros: Boolean = config("show_zeros", default = false)
+  var isCounts: Boolean = config("is_counts", default = false)
+
+  var minScore: Option[Double] = config("min_score")
+  var minLength: Option[Int] = config("min_length")
+
+  override def defaultCoreMemory = 4.0
+
+  executable = config("exe", default = "centrifuge-kreport", freeVar = false)
+
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    deps :+= new File(index + ".1.cf")
+    deps :+= new File(index + ".2.cf")
+    deps :+= new File(index + ".3.cf")
+  }
+
+  def cmdLine = executable +
+    conditional(onlyUnique, "--only-unique") +
+    conditional(showZeros, "--show-zeros") +
+    conditional(isCounts, "--is-counts") +
+    optional("--min-score=", minScore, spaceSeparated = false) +
+    optional("--min-length=", minLength, spaceSeparated = false) +
+    required("-x", index) +
+    repeat(centrifugeOutputFiles) +
+    " > " + required(output)
+}

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala

@@ -42,7 +42,7 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFunction wit
   @Output(doc = "Output JSON", shortName = "output", required = true)
   var output: File = _
 
-  override def defaultCoreMemory = 2.0
+  override def defaultCoreMemory = 4.0
 
   override def cmdLine =
     super.cmdLine +

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

@@ -19,7 +19,7 @@ import java.io.File
 import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, VcfUtils }
 
 import scala.collection.JavaConversions._
 import scala.io.Source
@@ -315,11 +315,11 @@ object VcfFilter extends ToolCommand {
    * Checks if given samples does have a variant hin this record
    *
    * @param record VCF record
-   * @param mustHaveVariant List of samples that should have this variant
+   * @param samples List of samples that should have this variant
    * @return true if filter passed
    */
-  def mustHaveVariant(record: VariantContext, mustHaveVariant: List[String]): Boolean = {
-    !mustHaveVariant.map(record.getGenotype).exists(a => a.isHomRef || a.isNoCall)
+  def mustHaveVariant(record: VariantContext, samples: List[String]): Boolean = {
+    !samples.map(record.getGenotype).exists(a => a.isHomRef || a.isNoCall || VcfUtils.isCompoundNoCall(a))
   }
 
   /** Checks if given samples have the same genotype */

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala

@@ -39,7 +39,9 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
   }
 
   val veppedPath = resourcePath("/VEP_oneline.vcf")
+  val starPath = resourcePath("/star_genotype.vcf.gz")
   val vepped = new File(veppedPath)
+  val star = new File(starPath)
   val rand = new Random()
 
   @Test def testOutputTypeVcf() = {
@@ -183,6 +185,9 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
     mustHaveVariant(record, List("Sample_101")) shouldBe true
     mustHaveVariant(record, List("Sample_101", "Sample_102")) shouldBe true
     mustHaveVariant(record, List("Sample_101", "Sample_102", "Sample_103")) shouldBe false
+
+    val starReader = new VCFFileReader(star, false)
+    starReader.iterator().foreach(x => mustHaveVariant(x, List("Sample_101")) shouldBe false)
   }
 
   @Test def testSameGenotype() = {

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala

@@ -140,4 +140,13 @@ object VcfUtils {
     reader.close()
     !hasNext
   }
+
+  /**
+   * Check whether genotype is of the form 0/.
+   * @param genotype genotype
+   * @return boolean
+   */
+  def isCompoundNoCall(genotype: Genotype): Boolean = {
+    genotype.isCalled && genotype.getAlleles.exists(_.isNoCall) && genotype.getAlleles.exists(_.isReference)
+  }
 }

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala

@@ -64,4 +64,30 @@ package object utils {
     case _ if fallBack => Try(raw)
     case _             => Try(throw new Exception(s"Can not extract number from string $raw"))
   }
+
+  val semanticVersionRegex = "(\\d+)\\.(\\d+)\\.(\\d+)(-.*)?".r
+
+  /**
+   * Check whether a version string is a semantic version.
+   *
+   * @param version version string
+   * @return boolean
+   */
+  def isSemanticVersion(version: String): Boolean = getSemanticVersion(version).isDefined
+
+  case class SemanticVersion(major: Int, minor: Int, patch: Int, build: Option[String] = None)
+  /**
+   * Check whether a version string is a semantic version.
+   * Note: the toInt calls here are only safe because the regex only matches numbers
+   *
+   * @param version version string
+   * @return SemanticVersion case class
+   */
+  def getSemanticVersion(version: String) = {
+    version match {
+      case semanticVersionRegex(major, minor, patch, build) =>
+        Some(SemanticVersion(major.toInt, minor.toInt, patch.toInt, Option(build).map(x => x.stripPrefix("-"))))
+      case _ => None
+    }
+  }
 }

biopet-utils/src/test/scala/VcfUtilsTest.scala

+import htsjdk.variant.variantcontext.{ Allele, Genotype, GenotypeBuilder }
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.JavaConversions._
+
+import nl.lumc.sasc.biopet.utils.VcfUtils
+
+/**
+ * Created by Sander Bollen on 4-10-16.
+ */
+class VcfUtilsTest extends TestNGSuite with Matchers {
+
+  @Test
+  def testCompoundNoCall(): Unit = {
+    val noAllele = Allele.NO_CALL
+    val refAllele = Allele.create("A", true)
+    val compoundNoCall = GenotypeBuilder.create("sample_01", List(noAllele, refAllele))
+    VcfUtils.isCompoundNoCall(compoundNoCall) shouldBe true
+
+    val altAllele = Allele.create("G", false)
+    val normalGenotype = GenotypeBuilder.create("sample_01", List(refAllele, altAllele))
+    VcfUtils.isCompoundNoCall(normalGenotype) shouldBe false
+
+    val completeNoCall = GenotypeBuilder.create("sample_01", List(noAllele, noAllele))
+    VcfUtils.isCompoundNoCall(completeNoCall) shouldBe false
+  }
+
+}

biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala

+package nl.lumc.sasc.biopet.utils
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by Sander Bollen on 12-10-16.
+ */
+class UtilsTest extends TestNGSuite with Matchers {
+
+  val semanticVersion = "1.2.3"
+  val semanticVersionWithBuild = "1.2.3-alpha0.1"
+  val nonSemanticVersion = "v1222.1"
+
+  @Test
+  def testIsSemantic() = {
+    isSemanticVersion(semanticVersion) shouldBe true
+    isSemanticVersion(semanticVersionWithBuild) shouldBe true
+    isSemanticVersion(nonSemanticVersion) shouldBe false
+  }
+
+  @Test
+  def testMajorVersion() = {
+    getSemanticVersion(semanticVersion).map(_.major) shouldBe Some(1)
+    getSemanticVersion(semanticVersionWithBuild).map(_.major) shouldBe Some(1)
+  }
+
+  @Test
+  def testMinorVersion() = {
+    getSemanticVersion(semanticVersion).map(_.minor) shouldBe Some(2)
+    getSemanticVersion(semanticVersionWithBuild).map(_.minor) shouldBe Some(2)
+  }
+
+  @Test
+  def testPatchVersion() = {
+    getSemanticVersion(semanticVersion).map(_.patch) shouldBe Some(3)
+    getSemanticVersion(semanticVersionWithBuild).map(_.patch) shouldBe Some(3)
+  }
+
+  @Test
+  def testBuildVersion() = {
+    getSemanticVersion(semanticVersion).flatMap(_.build) shouldBe None
+    getSemanticVersion(semanticVersionWithBuild).flatMap(_.build) shouldBe Some("alpha0.1")
+  }
+}

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp

@@ -10,11 +10,13 @@
 <%@ var libId: Option[String] = None %>
 <%@ var args: Map[String, Any] %>
 <%@ var outputDir: File %>
+<%@ var summaryStatsTag: String = "krakenreport" %>
+<%@ var summaryModuleTag: String = "gearskraken" %>
 
 <%
     val summaries = if (sampleId.isEmpty && libId.isEmpty) {
-        summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
-    } else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
+        summary.getSampleValues(summaryModuleTag, "stats", summaryStatsTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
+    } else summary.getValue(sampleId, libId, summaryModuleTag, "stats", summaryStatsTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
 
     val tempFile = File.createTempFile("krona.", ".xml")
     tempFile.deleteOnExit()
@@ -24,10 +26,10 @@
     args ++ Map("kronaXml" -> tempFile))
 
 
-    val file = new File(outputDir, "kraken_krona.html")
+    val file = new File(outputDir, s"$summaryModuleTag-$summaryStatsTag.html")
     val writer = new PrintWriter(file)
     writer.println(output)
     writer.close()
 %>
 
-<iframe src="kraken_krona.html" style="width:100%;height:80vh;border:none;"></iframe>
+<iframe src="${summaryModuleTag}-${summaryStatsTag}.html" style="width:100%;height:80vh;border:none;"></iframe>

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

+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.tools.KrakenReportToJson
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 19/09/16.
+ */
+class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
+
+  var fastqR1: File = _
+
+  var fastqR2: Option[File] = None
+
+  var outputName: String = _
+
+  override def fixedValues = Map("centrifugekreport" -> Map("only_unique" -> false))
+
+  def init(): Unit = {
+    require(fastqR1 != null)
+    require(outputName != null)
+  }
+
+  def centrifugeOutput = new File(outputDir, s"$outputName.centrifuge.gz")
+
+  def biopetScript(): Unit = {
+    val centrifuge = new Centrifuge(this)
+    centrifuge.inputR1 = fastqR1
+    centrifuge.inputR2 = fastqR2
+    centrifuge.output = new File(outputDir, s"$outputName.centrifuge")
+    centrifuge.report = Some(new File(outputDir, s"$outputName.centrifuge.report"))
+    centrifuge.isIntermediate = true
+    add(centrifuge)
+
+    add(Gzip(this, centrifuge.output, centrifugeOutput))
+
+    makeKreport(List(centrifuge.output), "centrifuge", unique = false)
+    makeKreport(List(centrifuge.output), "centrifuge_unique", unique = true)
+
+    addSummaryJobs()
+  }
+
+  protected def makeKreport(inputFiles: List[File], name: String, unique: Boolean): Unit = {
+    val centrifugeKreport = new CentrifugeKreport(this)
+    centrifugeKreport.centrifugeOutputFiles = inputFiles
+    centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
+    centrifugeKreport.onlyUnique = unique
+    add(centrifugeKreport)
+
+    val krakenReportJSON = new KrakenReportToJson(this)
+    krakenReportJSON.inputReport = centrifugeKreport.output
+    krakenReportJSON.output = new File(outputDir, s"$outputName.$name.krkn.json")
+    krakenReportJSON.skipNames = config("skipNames", default = false)
+    add(krakenReportJSON)
+    addSummarizable(krakenReportJSON, s"${name}_report")
+  }
+
+  /** Location of summary file */
+  def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".centrifuge.summary.json")
+
+  /** Pipeline settings shown in the summary file */
+  def summarySettings: Map[String, Any] = Map()
+
+  /** Statistics shown in the summary file */
+  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/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala

@@ -41,10 +41,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
 
   def init(): Unit = {
     require(fastqR1 != null)
-    if (outputName == null) outputName = fastqR1.getName
-      .stripSuffix(".gz")
-      .stripSuffix(".fq")
-      .stripSuffix(".fastq")
+    require(outputName != null)
   }
 
   lazy val krakenConvertToFasta: Boolean = config("kraken_discard_quality", default = false)
@@ -107,7 +104,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
   def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".kraken.summary.json")
 
   /** Pipeline settings shown in the summary file */
-  def summarySettings: Map[String, Any] = Map.empty
+  def summarySettings: Map[String, Any] = Map()
 
   /** Statistics shown in the summary file */
   def summaryFiles: Map[String, File] = outputFiles + ("input_R1" -> fastqR1) ++ (fastqR2 match {

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

@@ -38,13 +38,20 @@ object GearsReport extends MultisampleReportBuilder {
 
   def indexPage = {
     val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
+    val centrifugeExecuted = summary.getSampleValues("gearscentrifuge", "stats", "centrifuge_report").values.forall(_.isDefined)
     val qiimeClosesOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_closed_otu_table", "path")
       .map(x => new File(x.toString))
     val qiimeOpenOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_open_otu_table", "path")
       .map(x => new File(x.toString))
 
     ReportPage(
-      (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
+      (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+        Map("summaryStatsTag" -> "centrifuge_report")
+      )), Map())), List(
+        "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+          Map("summaryStatsTag" -> "centrifuge_unique_report")
+        )), Map("summaryModuleTag" -> "gearscentrifuge")))
+      else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
         "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
@@ -74,12 +81,19 @@ object GearsReport extends MultisampleReportBuilder {
   /** Single sample page */
   def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
     val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined
+    val centrifugeExecuted = summary.getValue(Some(sampleId), None, "gearscentrifuge", "stats", "centrifuge_report").isDefined
     val qiimeClosesOtuTable = summary.getValue(Some(sampleId), None, "gearsqiimeclosed", "files", "pipeline", "otu_table", "path")
       .map(x => new File(x.toString))
     val qiimeOpenOtuTable = summary.getValue(Some(sampleId), None, "gearsqiimeopen", "files", "pipeline", "otu_table", "path")
       .map(x => new File(x.toString))
 
-    ReportPage((if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
+    ReportPage((if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+      Map("summaryStatsTag" -> "centrifuge_report")
+    )), Map())), List(
+      "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+        Map("summaryStatsTag" -> "centrifuge_unique_report")
+      )), Map("summaryModuleTag" -> "gearscentrifuge")))
+    else Nil) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
       "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
       )), Map()))
     else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
@@ -99,6 +113,7 @@ object GearsReport extends MultisampleReportBuilder {
   def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
     val flexiprepExecuted = summary.getLibraryValue(sampleId, libId, "flexiprep").isDefined
     val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
+    val centrifugeExecuted = summary.getValue(Some(sampleId), Some(libId), "gearscentrifuge", "stats", "centrifuge_report").isDefined
     val qiimeClosesOtuTable = summary.getValue(Some(sampleId), Some(libId), "gearsqiimeclosed", "files", "pipeline", "otu_table", "path")
       .map(x => new File(x.toString))
     val qiimeOpenOtuTable = summary.getValue(Some(sampleId), Some(libId), "gearsqiimeopen", "files", "pipeline", "otu_table", "path")
@@ -106,7 +121,13 @@ object GearsReport extends MultisampleReportBuilder {
 
     ReportPage(
       (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
-      ) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
+      ) ::: (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+        Map("summaryStatsTag" -> "centrifuge_report")
+      )), Map())), List(
+        "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+          Map("summaryStatsTag" -> "centrifuge_unique_report")
+        )), Map("summaryModuleTag" -> "gearscentrifuge")))
+      else Nil) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
         "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(

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

@@ -41,6 +41,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   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 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
@@ -126,6 +127,14 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
       add(kraken)
     }
 
+    centrifugeScript foreach { centrifuge =>
+      centrifuge.outputDir = new File(outputDir, "centrifuge")
+      centrifuge.fastqR1 = r1
+      centrifuge.fastqR2 = r2
+      centrifuge.outputName = outputName
+      add(centrifuge)
+    }
+
     qiimeRatx foreach { qiimeRatx =>
       qiimeRatx.outputDir = new File(outputDir, "qiime_rtax")
       qiimeRatx.fastqR1 = r1

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

@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
 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.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
@@ -49,6 +51,7 @@ 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 +64,7 @@ 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,
@@ -102,12 +106,15 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
         gears.outputName shouldBe (if (inputMode == Some("bam")) "bamfile" else "R1")