XhmmGenotype.scala 1.56 KB
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/**
 * 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.
 */
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package nl.lumc.sasc.biopet.extensions.xhmm

import java.io.File

import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
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import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
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/**
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 * Created by Sander Bollen on 23-11-16.
 */
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class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {

  @Input
  var inputMatrix: File = _

  @Input
  var inputXcnv: File = _

  @Output
  var outputVcf: File = _

  @Input
  var r: File = _

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  @Input
  var f: File = _

  override def beforeGraph() = {
    super.beforeGraph()
    if (f == null) {
      f = referenceFasta()
    }
  }
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  def cmdLine = {
    executable + required("--genotype") +
      required("-p", discoverParamsFile) +
      required("-r", inputMatrix) +
      required("-R", r) +
      required("-g", inputXcnv) +
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      required("-F", f) +
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      required("-v", outputVcf)
  }

}