Commit 34f97a24 authored by Peter van 't Hof's avatar Peter van 't Hof

Switch to only 1 maven artifact as example

parent 6f608545
......@@ -4,21 +4,42 @@
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>
<groupId>nl.lumc.kg</groupId>
<!--TODO: replace groupId -->
<groupId>org.example.group</groupId>
<!--TODO: replace artifactId -->
<artifactId>SinglePipeline</artifactId>
<!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
<version>0.5.0-DEV</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<scoverage.plugin.version>1.0.4</scoverage.plugin.version>
<sting.shade.phase>package</sting.shade.phase>
<app.main.class>org.example.group.SinglePipeline</app.main.class>
<!--TODO: replace app.main.class, this is the class that get executed when running the jar file -->
<app.main.class>org.example.group.BiopetPipeline</app.main.class>
</properties>
<dependencies>
<!--
In here maven dependencies can be placed, when importing a biopet pipeline 'Biopet-Framework' is not required.
When only using the framework without pipeline you need to import BiopetFramework.
It's advised to not use different versions of the pipeline and the framework.
-->
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<!--TODO: replace version of pipeline to a fixed version -->
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Shiva</artifactId>
<!--TODO: replace version of pipeline to a fixed version -->
<version>${project.version}</version>
</dependency>
</dependencies>
......
......@@ -9,26 +9,36 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 8/28/15.
*/
class SinglePipeline(val root: Configurable) extends QScript with SummaryQScript {
//TODO: Replace class Name
class BiopetPipeline(val root: Configurable) extends QScript with SummaryQScript {
def this() = this(null)
/** Only required when using [[SummaryQScript]] */
def summaryFile = new File(outputDir, "magpie.summary.json")
/** Only required when using [[SummaryQScript]] */
def summaryFiles: Map[String, File] = Map()
/** Only required when using [[SummaryQScript]] */
def summarySettings = Map()
// This method can be used to initialize some classes where needed
def init(): Unit = {
}
// This method is the actual pipeline
def biopetScript: Unit = {
// Executing a biopet pipeline inside
val shiva = new Shiva(this)
shiva.init()
shiva.biopetScript()
addAll(shiva.functions)
/* Only required when using [[SummaryQScript]] */
addSummaryQScript(shiva)
}
}
object SinglePipeline extends PipelineCommand
//TODO: Replace object Name, must be the same as the class of the pipeline
object BiopetPipeline extends PipelineCommand
<?xml version="1.0" encoding="UTF-8"?>
<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">
<parent>
<artifactId>BiopetRoot</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.5.0-DEV</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<packaging>pom</packaging>
<artifactId>ExternalExamples</artifactId>
<modules>
<module>single-pipeline</module>
</modules>
</project>
\ No newline at end of file
......@@ -16,6 +16,6 @@
<modules>
<module>public</module>
<module>protected</module>
<module>external-examples</module>
<module>external-example</module>
</modules>
</project>
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