Commit 6f608545 authored by Peter van 't Hof's avatar Peter van 't Hof

Added single pipeline example

parent 59b8f961
<?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
# Project-related
dependency-reduced-pom.xml
git.properties
# gedit
*~
# Vim
*.swp
# IntelliJ
.idea/*
*.iml
target/
public/target/
protected/target/
Test implementation of Magpie 2.0
\ No newline at end of file
This diff is collapsed.
package org.example.group
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 8/28/15.
*/
class SinglePipeline(val root: Configurable) extends QScript with SummaryQScript {
def this() = this(null)
def summaryFile = new File(outputDir, "magpie.summary.json")
def summaryFiles: Map[String, File] = Map()
def summarySettings = Map()
def init(): Unit = {
}
def biopetScript: Unit = {
val shiva = new Shiva(this)
shiva.init()
shiva.biopetScript()
addAll(shiva.functions)
addSummaryQScript(shiva)
}
}
object SinglePipeline extends PipelineCommand
......@@ -16,5 +16,6 @@
<modules>
<module>public</module>
<module>protected</module>
<module>external-examples</module>
</modules>
</project>
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment