Commit f5753766 authored by Sander Bollen's avatar Sander Bollen

tarmac pipeline skeleton

parent 2299e7a9
...@@ -38,6 +38,7 @@ ...@@ -38,6 +38,7 @@
<module>mapping</module> <module>mapping</module>
<module>sage</module> <module>sage</module>
<module>shiva</module> <module>shiva</module>
<module>tarmac</module>
<module>tinycap</module> <module>tinycap</module>
<module>toucan</module> <module>toucan</module>
<module>biopet-core</module> <module>biopet-core</module>
......
<!--
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 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>Tarmac</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2017</inceptionYear>
<name>Tarmac</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>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
package nl.lumc.sasc.biopet.pipelines.tarmac
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
* Created by Sander Bollen on 23-3-17.
*/
class Tarmac(val root: Configurable) extends QScript with SummaryQScript with Reference {
qscript =>
def this() = this(null)
def init() = {
}
def biopetScript() = {
}
def summarySettings: Map[String, Any] = Map()
def summaryFiles: Map[String, File] = Map()
def summaryFile: File = new File(outputDir, "tarmac.summary.json")
}
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