CentrifugeKreport.scala 868 Bytes
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package nl.lumc.sasc.biopet.extensions.centrifuge

import java.io.File

import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
Peter van 't Hof's avatar
Peter van 't Hof committed
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import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
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/**
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 * Created by pjvanthof on 19/09/16.
 */
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class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunction {
  @Input(doc = "Output files centrifuge", required = true)
  var centrifugeOutputFiles: List[File] = Nil

  @Output(doc = "Output report")
  var output: File = _

  @Input(doc = "Centrifuge index prefix", required = true)
  var index: File = config("centrifige_index", namespace = "centrifuge")

  executable = config("exe", default = "centrifuge-kreport", freeVar = false)

  def cmdLine = executable +
    //TODO: Options
    required("-x", index) +
    repeat(centrifugeOutputFiles)
}