Added pipeline to agregation and executable

biopet-aggregate/pom.xml

@@ -17,6 +17,7 @@
 
     <modules>
         <module>../biopet-core</module>
+        <module>../generate-indexes</module>
         <module>../biopet-package</module>
         <module>../bammetrics</module>
         <module>../flexiprep</module>

biopet-package/pom.xml

@@ -44,6 +44,11 @@
             <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>GenerateIndexes</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Flexiprep</artifactId>

biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

@@ -35,7 +35,8 @@ object BiopetExecutableMain extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest,
     nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
     nl.lumc.sasc.biopet.pipelines.basty.Basty,
-    nl.lumc.sasc.biopet.pipelines.shiva.Shiva
+    nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
+    nl.lumc.sasc.biopet.pipelines.GenerateIndexes
   )
 
   def tools: List[MainCommand] = BiopetToolsExecutable.tools