Move generate indexes to own maven artifact

public/generate-indexes/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Biopet is built on top of GATK Queue for building bioinformatic
+    pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+    SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+    should also be able to execute Biopet tools and pipelines.
+
+    Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+
+    Contact us at: sasc@lumc.nl
+
+    A dual licensing mode is applied. The source code within this project that are
+    not part of GATK Queue is freely available for non-commercial use under an AGPL
+    license; For commercial users or users who do not want to follow the AGPL
+    license, please contact us to obtain a separate license.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>GenerateIndexes</artifactId>
+    <packaging>jar</packaging>
+
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.5.0-DEV</version>
+        <relativePath>../</relativePath>
+    </parent>
+
+    <inceptionYear>2014</inceptionYear>
+    <name>GenerateIndexes</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+</project>
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala → public/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala

@@ -18,18 +18,18 @@ package nl.lumc.sasc.biopet.pipelines
 import java.io.PrintWriter
 import java.util
 
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, PipelineCommand, BiopetQScript }
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2Build, BowtieBuild }
 import nl.lumc.sasc.biopet.extensions.bwa.BwaIndex
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.gmap.GmapBuild
 import nl.lumc.sasc.biopet.extensions.picard.CreateSequenceDictionary
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFaidx
-import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.Input
+
 import scala.collection.JavaConversions._
 
 class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript {

public/pom.xml

@@ -40,6 +40,7 @@
 	    <module>toucan</module>
         <module>shiva</module>
         <module>basty</module>
+        <module>generate-indexes</module>
     </modules>
 
     <properties>