GearsSeqCount.scala 1.48 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
 *
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 * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
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 * 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.pipelines.gears

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import nl.lumc.sasc.biopet.core.{ BiopetQScript, SampleLibraryTag }
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import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.tools.SageCountFastq
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript

/**
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 * Created by pjvan_thof on 12/29/15.
 */
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class GearsSeqCount(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag {

  var fastqInput: File = _

  def countFile = swapExt(outputDir, fastqInput, ".fastq.gz", ".counts.txt")

  /** Init for pipeline */
  def init(): Unit = {
  }

  /** Pipeline itself */
  def biopetScript(): Unit = {
    val seqCount = new SageCountFastq(this)
    seqCount.input = fastqInput
    seqCount.output = countFile
    add(seqCount)
  }
}