Fixed last unit tests

generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala

@@ -29,10 +29,10 @@ import org.testng.annotations.{ AfterClass, Test }
  * Created by pjvan_thof on 13-5-16.
  */
 class DownloadGenomesTest extends TestNGSuite with Matchers {
-  def initPipeline(map: Map[String, Any], outputDir: File): DownloadGenomes = {
+  def initPipeline(map: Map[String, Any], dir: File): DownloadGenomes = {
     new DownloadGenomes() {
       override def configNamespace = "generateindexes"
-      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, DownloadGenomesTest.config(outputDir)))
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, DownloadGenomesTest.config(dir)))
       qSettings = new QSettings
       qSettings.runName = "test"
     }

tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala

@@ -102,9 +102,9 @@ object TinyCapTest {
   def outputDir = Files.createTempDir()
   val inputDir = Files.createTempDir()
 
-  val r1 = new File(inputDir, "input" + File.separator + "R1.fq.gz")
+  val r1 = new File(inputDir, "R1.fq.gz")
   Files.touch(r1)
-  val bam = new File(inputDir, "input" + File.separator + "bamfile.bam")
+  val bam = new File(inputDir, "bamfile.bam")
   Files.touch(bam)
 
   val referenceFasta = new File(inputDir, "ref.fa")