From f7166e1889f50d04b95c3c5fc245a8d0247c1107 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 2 Mar 2017 19:19:58 +0100
Subject: [PATCH] Fixed unit tests for shiva

---
 .../nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala     | 1 -
 .../lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala | 4 ++--
 .../scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala | 2 +-
 .../sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala | 4 ++--
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala b/kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
index d16dc1989..45d797798 100644
--- a/kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala
+++ b/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"
     }
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
index 6a7423bc8..83caa7c64 100644
--- a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+++ b/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"
     }
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index f3fa0433f..f5fce6c4a 100644
--- a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/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()
   }
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index c822399f9..5914de186 100644
--- a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/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"
     }
-- 
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