Added empty pipeline for gwas test

public/gwas-test/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>GwasTest</artifactId>
+    <packaging>jar</packaging>
+
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.6.0-SNAPSHOT</version>
+        <relativePath>../</relativePath>
+    </parent>
+
+    <inceptionYear>2014</inceptionYear>
+    <name>GwasTest</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetCore</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetExtensions</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+</project>
\ No newline at end of file

public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala

+package nl.lumc.sasc.biopet.pipelines.gwastest
+
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvanthof on 16/03/16.
+  */
+class GwasTest(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  /** Init for pipeline */
+  def init(): Unit = {
+  }
+
+  /** Pipeline itself */
+  def biopetScript(): Unit = {
+
+  }
+}

public/pom.xml

@@ -25,7 +25,6 @@
     <version>0.6.0-SNAPSHOT</version>
     
     <modules>
-        <!--<module>biopet-framework</module>-->
         <module>biopet-public-package</module>
         <module>bam2wig</module>
         <module>bammetrics</module>
@@ -47,6 +46,7 @@
         <module>biopet-tools-extensions</module>
         <module>biopet-extensions</module>
         <module>biopet-tools-package</module>
+        <module>gwas-test</module>
     </modules>
 
     <properties>