Commit 7e6ef439 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding centrifuge to testing

parent deced04c
......@@ -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)
......
......@@ -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
......
......@@ -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)
......
......@@ -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
......
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