Fixed unit tests for shiva

kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala

@@ -38,7 +38,6 @@ class KopisuTest extends TestNGSuite with Matchers {
     new Kopisu() {
       override def configNamespace = "kopisu"
       override def globalConfig = new Config(ConfigUtils.mergeMaps(map, KopisuTest.config(dir)))
-      outputDir = dir
       qSettings = new QSettings
       qSettings.runName = "test"
     }

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

@@ -38,10 +38,10 @@ import scala.collection.mutable.ListBuffer
  * Created by pjvan_thof on 3/2/15.
  */
 class ShivaSvCallingTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any], outputDir: File): ShivaSvCalling = {
+  def initPipeline(map: Map[String, Any], dir: File): ShivaSvCalling = {
     new ShivaSvCalling {
       override def configNamespace = "shivasvcalling"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config(outputDir)))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config(dir)))
       qSettings = new QSettings
       qSettings.runName = "test"
     }

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

@@ -193,7 +193,7 @@ object ShivaTest {
 
   private def copyFile(name: String): Unit = {
     val is = getClass.getResourceAsStream("/" + name)
-    val os = new FileOutputStream(new File(outputDir, name))
+    val os = new FileOutputStream(new File(inputDir, name))
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }

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

@@ -44,10 +44,10 @@ import scala.collection.mutable.ListBuffer
  * Created by pjvan_thof on 3/2/15.
  */
 trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any], outputDir: File): ShivaVariantcalling = {
+  def initPipeline(map: Map[String, Any], dir: File): ShivaVariantcalling = {
     new ShivaVariantcalling() {
       override def configNamespace = "shivavariantcalling"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config(outputDir)))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config(dir)))
       qSettings = new QSettings
       qSettings.runName = "test"
     }