Added aggregate option for scoverage

pom.xml

@@ -17,6 +17,6 @@
         <module>public</module>
         <module>protected</module>
         <module>external-example</module>
-        <module>biopet-aggregate</module>
+        <!--<module>biopet-aggregate</module>-->
     </modules>
 </project>

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -94,7 +94,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
       if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
       else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
     }
-    
+
     this match {
       case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
         logger.info("Write report is skipped because sample flag is used")

public/pom.xml

@@ -51,6 +51,7 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
+        <scalaVersion>2.10.4</scalaVersion>
     </properties>
     
     <build>
@@ -243,14 +244,10 @@
               <artifactId>scoverage-maven-plugin</artifactId>
               <version>${scoverage.plugin.version}</version>
               <configuration>
-                  <scalaVersion>2.10.2</scalaVersion>
+                  <scalaVersion>${scalaVersion}</scalaVersion>
+                  <aggregate>true</aggregate>
                   <!-- other parameters -->
               </configuration>
-              <executions>
-                  <execution>
-                      <phase>test</phase>
-                  </execution>
-              </executions>
             </plugin>
       </plugins>
     </build>