well.. it compiles

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

@@ -85,7 +85,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Vers
 
   /** return commandline to execute */
   def cmdLine = required(executable) +
-    optional("--java", java_exe) +
+    optional("--java", javaExe) +
     optional("--threads", threads) +
     optional("--contaminants", contaminants) +
     optional("--adapters", adapters) +

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

@@ -35,7 +35,7 @@ class TinyCapTest extends TestNGSuite with Matchers {
 
   def initPipeline(map: Map[String, Any]): TinyCap = {
     new TinyCap() {
-      override def configName = "tinycap"
+      override def configNamespace = "tinycap"
 
       override def globalConfig = new Config(map)