Fix output dirs

public/flexiprep/Flexiprep.iml

@@ -6,6 +6,8 @@
     <content url="file://$MODULE_DIR$">
       <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
       <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" />
       <excludeFolder url="file://$MODULE_DIR$/target" />
     </content>
     <orderEntry type="inheritedJdk" />
@@ -16,7 +18,6 @@
     <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
     <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
     <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
-    <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
     <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
     <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
     <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
@@ -82,11 +83,19 @@
     <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
     <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
     <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
-    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
     <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
     <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
     <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
     <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
     <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" />
+    <orderEntry type="library" name="Maven: junit:junit:4.10" level="project" />
+    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
   </component>
 </module>
\ No newline at end of file

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -176,7 +176,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
       var R2 = fastqfile._2
       var deps: List[File] = Nil
       if (!skipFlexiprep) {
-        val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunkDir)
+        val flexiout = flexiprep.runTrimClip(R1, R2, new File(chunkDir, "flexiprep"), chunkDir)
         logger.debug(chunkDir + " - " + flexiout)
         R1 = flexiout._1
         if (paired) R2 = flexiout._2