Commit 6e66f2cc authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed unit tests

parent 0abb015b
......@@ -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()
......
......@@ -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)
}
......
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