ValidateFastq.scala 1.35 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 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.tools

import java.io.File

import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}

class ValidateFastq(val root: Configurable) extends ToolCommandFunction {
  def toolObject = nl.lumc.sasc.biopet.tools.ValidateFastq

  @Input(doc = "Input R1 fastq file", required = true)
  var r1Fastq: File = _

  @Input(doc = "Input R1 fastq file", required = false)
  var r2Fastq: Option[File] = None

  override def cmdLine = super.cmdLine +
    required("-i", r1Fastq) +
    optional("-j", r2Fastq)
}