Fix threading issue in unit tests

public/biopet-tools-extensions/src/test/scala/VcfFilterTest.scala

@@ -3,12 +3,11 @@ import java.io.File
 import nl.lumc.sasc.biopet.extensions.tools.VcfFilter
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{DataProvider, Test}
-
+import org.testng.annotations.{ DataProvider, Test }
 
 /**
-  * Created by ahbbollen on 2-3-16.
-  */
+ * Created by ahbbollen on 2-3-16.
+ */
 class VcfFilterTest extends TestNGSuite with Matchers {
 
   def cmd(s: String) = {
@@ -112,7 +111,7 @@ class VcfFilterTest extends TestNGSuite with Matchers {
     }
 
     if (minAlternateDepth.isDefined) {
-     cmdString = "--minAlternateDepth " + minAlternateDepth.getOrElse("") :: cmdString
+      cmdString = "--minAlternateDepth " + minAlternateDepth.getOrElse("") :: cmdString
     }
 
     if (minSamplesPass.isDefined) {
@@ -183,7 +182,6 @@ class VcfFilterTest extends TestNGSuite with Matchers {
       cmdString = "--minQualScore " + minQualScore.getOrElse("") :: cmdString
     }
 
-
     cmdString.foreach(x => command.contains(x) shouldBe true)
   }
 

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala

@@ -30,7 +30,7 @@ import scala.sys.process.{ Process, ProcessLogger }
 trait Rscript extends Configurable {
   protected var script: File
 
-  def rscriptExecutable: String = config("exe", default = "Rscript", submodule = "Rscript")
+  def rscriptExecutable: String = config("exe", default = "Rscript", submodule = "rscript")
 
   /** This is the defaul implementation, to add arguments override this */
   def cmd: Seq[String] = Seq(rscriptExecutable, script.getAbsolutePath)

public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -15,18 +15,17 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.tools.BaseCounter
-import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions._
+import nl.lumc.sasc.biopet.extensions.tools.BaseCounter
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.apache.commons.io.FileUtils
+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.{ AfterClass, DataProvider, Test }
+import org.testng.annotations.{DataProvider, Test}
 
 abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNGSuite with Matchers {
 
@@ -143,10 +142,6 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
     }
   }
 
-  // remove temporary run directory all tests in the class have been run
-  @AfterClass def removeTempOutputDir() = {
-    FileUtils.deleteDirectory(GentrapTest.outputDir)
-  }
 }
 
 class GentrapFragmentsPerGeneTest extends GentrapTestAbstract("fragments_per_gene")
@@ -158,6 +153,7 @@ class GentrapCufflinksBlindTest extends GentrapTestAbstract("cufflinks_blind")
 
 object GentrapTest {
   val outputDir = Files.createTempDir()
+  outputDir.deleteOnExit()
   new File(outputDir, "input").mkdirs()
   def inputTouch(name: String): String = {
     val file = new File(outputDir, "input" + File.separator + name)
@@ -182,7 +178,8 @@ object GentrapTest {
     "annotation_gtf" -> (outputDir + File.separator + "ref.fa"),
     "annotation_bed" -> (outputDir + File.separator + "ref.fa"),
     "annotation_refflat" -> (outputDir + File.separator + "ref.fa"),
-    "varscan_jar" -> "test"
+    "varscan_jar" -> "test",
+    "rscript" -> Map("exe" -> "test")
   ) ++ Seq(
       // fastqc executables
       "fastqc", "seqtk", "sickle", "cutadapt",

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

@@ -133,6 +133,8 @@ object ShivaVariantcallingTest {
     "md5sum" -> Map("exe" -> "test"),
     "bgzip" -> Map("exe" -> "test"),
     "tabix" -> Map("exe" -> "test"),
+    "rscript" -> Map("exe" -> "test"),
+    "exe" -> "test",
     "varscan_jar" -> "test"
   )
 }
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