Added centrifuge to Gears

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

@@ -4,7 +4,7 @@ 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 org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.util.matching.Regex
 

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

@@ -4,7 +4,7 @@ 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}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
   * Created by pjvanthof on 19/09/16.

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.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 = _
+
+  def init(): Unit = {
+    require(fastqR1 != null)
+    if (outputName == null) outputName = fastqR1.getName
+      .stripSuffix(".gz")
+      .stripSuffix(".fq")
+      .stripSuffix(".fastq")
+  }
+
+  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"))
+    add(centrifuge)
+
+    val centrifugeKreport = new CentrifugeKreport(this)
+    centrifugeKreport.centrifugeOutputFiles += centrifuge.output
+    centrifugeKreport.output = new File(outputDir, s"$outputName.centrifuge.kreport")
+    add(centrifugeKreport)
+
+    val krakenReportJSON = new KrakenReportToJson(this)
+    krakenReportJSON.inputReport = centrifugeKreport.output
+    krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
+    krakenReportJSON.skipNames = config("skipNames", default = false)
+    add(krakenReportJSON)
+    addSummarizable(krakenReportJSON, "centrifugereport")
+  }
+
+  /** Location of summary file */
+  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()
+
+  /** 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()
+  })
+
+}

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

@@ -107,7 +107,7 @@ 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/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