From c749c1a3f7c1aee6a68028628f3c5693a4d2b9f2 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 16 Mar 2016 20:50:09 +0100
Subject: [PATCH] Added empty pipeline for gwas test
---
public/gwas-test/pom.xml | 50 +++++++++++++++++++
.../biopet/pipelines/gwastest/GwasTest.scala | 21 ++++++++
public/pom.xml | 2 +-
3 files changed, 72 insertions(+), 1 deletion(-)
create mode 100644 public/gwas-test/pom.xml
create mode 100644 public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
diff --git a/public/gwas-test/pom.xml b/public/gwas-test/pom.xml
new file mode 100644
index 000000000..84d4fc015
--- /dev/null
+++ b/public/gwas-test/pom.xml
@@ -0,0 +1,50 @@
+<?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
diff --git a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
new file mode 100644
index 000000000..66137988e
--- /dev/null
+++ b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala
@@ -0,0 +1,21 @@
+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 = {
+
+ }
+}
diff --git a/public/pom.xml b/public/pom.xml
index f5a23c9cd..9bc3ce5cf 100644
--- a/public/pom.xml
+++ b/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>
--
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