Commit 241a7d23 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added vt normalizer extension

parent 1568a600
/**
* 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.vt
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
/**
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
abstract class Vt extends BiopetCommandLineFunction {
override def subPath = "vt" :: super.subPath
executable = config("exe", default = "vt")
}
package nl.lumc.sasc.biopet.extensions.vt
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, Version}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
/**
* Created by pjvanthof on 20/11/15.
*/
class VtNormalize(val root: Configurable) extends Vt with Version with Reference {
def versionRegex = """normalize (.*)""".r
override def versionExitcode = List(0, 1)
def versionCommand = executable + " normalize"
@Input(required = true)
var inputVcf: File = _
@Output(required = true)
var outputVcf: File = _
var windowSize: Option[Int] = config("windows_size")
var intervalsFile: Option[File] = config("intervals_file")
var reference: File = _
override def beforeGraph(): Unit = {
super.beforeGraph()
reference = referenceFasta()
}
def cmdLine = required(executable) + required("normalize") +
required("-o", outputVcf) +
optional("-w", windowSize) +
optional("-I", intervalsFile) +
required("-r", reference)
required(inputVcf)
}
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