Commit a878479e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added a template as example

parent 55378379
/**
* 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.
*/
package nl.lumc.sasc.biopet.pipelines
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript, BiopetQScript }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QScript
class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
class Sample(val sampleId: String) extends AbstractSample {
val libraries: Map[String, Library] = getLibrariesIds.map(id => id -> new Library(id)).toMap
class Library(val libraryId: String) extends AbstractLibrary {
def runJobs(): Unit = {
// Library jobs
}
}
def runJobs(): Unit = {
// Sample jobs
}
}
def init(): Unit = {
samples = getSamplesIds.map(id => id -> new Sample(id)).toMap
}
def biopetScript() {
}
}
object MultisamplePipelineTemplate extends PipelineCommand
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