Commit 571223aa authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove unused source

parent a5ecd049
/**
* 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.extensions.clever
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
class Clever(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
@Input(doc = "Input file (bam)")
var input: File = _
@Input(doc = "Reference")
var reference: File = _
@Argument(doc = "Work directory")
var workdir: String = _
@Argument(doc = "Current working directory")
var cwd: String = _
override def init() {
}
def biopetScript() {
// write the pipeline here
logger.info("Starting Clever Pipeline")
/// start clever and then copy the vcf into the root directory "<sample>.clever/"
val clever = CleverCaller(this, input, reference, cwd, workdir)
outputFiles += ("clever_vcf" -> clever.outputvcf)
add(clever)
}
}
object Clever extends PipelineCommand {
override val pipeline = "/nl/lumc/sasc/biopet/extensions/svcallers/Clever/Clever.class"
def apply(root: Configurable, input: File, runDir: String): Clever = {
val cleverpipeline = new Clever(root)
cleverpipeline.input = input
cleverpipeline.workdir = runDir
cleverpipeline.init()
cleverpipeline.biopetScript()
cleverpipeline
}
}
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