Fixed tests

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala

@@ -15,20 +15,20 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 import java.nio.file.Paths
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
+import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerCaller, BreakdancerConfig, BreakdancerVCF}
 import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
 import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
-import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelConfig, PindelVCF }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelConfig, PindelVCF}
+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}
 
 import scala.collection.mutable.ListBuffer
 
@@ -152,9 +152,9 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
     pipeline.inputBams = Map("bam" -> ShivaSvCallingTest.inputTouch("bam" + ".bam"))
 
     intercept[IllegalArgumentException] {
-      pipeline.init()
       pipeline.script()
     }
+    Logging.errors.clear()
   }
 
   private def resourcePath(p: String): String = {

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -84,7 +84,7 @@ class ShivaTest extends TestNGSuite with Matchers {
       // Gatk preprocess
       pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
       pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
-      pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
+      pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
       pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
 
       pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (if (multi) 2 else 0)

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -15,7 +15,6 @@ import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.gatk.broad.{ HaplotypeCaller, UnifiedGenotyper }
 import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
@@ -53,9 +52,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
 
   @DataProvider(name = "shivaVariantcallingOptions")
   def shivaVariantcallingOptions = {
-    (for (
-      bams <- 0 to 2;
-    ) yield Array[Any](bams, raw, bcftools, bcftools_singlesample, unifiedGenotyper,
+    (for (bams <- 0 to 2) yield Array[Any](bams, raw, bcftools, bcftools_singlesample, unifiedGenotyper,
       haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele,
       freebayes, varscanCnsSinglesample)
     ).toArray
@@ -89,7 +86,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
 
     pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
 
-    val illegalArgumentException = pipeline.inputBams.isEmpty || (callers.isEmpty)
+    val illegalArgumentException = pipeline.inputBams.isEmpty || callers.isEmpty
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
       pipeline.script()
@@ -113,10 +110,6 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
       pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size)
     }
   }
-
-  @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
-  }
 }
 
 class ShivaVariantcallingNoVariantcallersTest extends ShivaVariantcallingTestTrait
@@ -165,6 +158,7 @@ class ShivaVariantcallingVarscanCnsSinglesampleTest extends ShivaVariantcallingT
 
 object ShivaVariantcallingTest {
   val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
   new File(outputDir, "input").mkdirs()
   def inputTouch(name: String): File = {
     val file = new File(outputDir, "input" + File.separator + name).getAbsoluteFile