Sambamba.scala 1.27 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.
 */
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package nl.lumc.sasc.biopet.extensions.sambamba

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import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
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/** General Sambamba extension */
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abstract class Sambamba extends BiopetCommandLineFunction with Version {
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  override def defaultCoreMemory = 4.0
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  override def defaultThreads = 2
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  override def subPath = "sambamba" :: super.subPath

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  executable = config("exe", default = "sambamba", submodule = "sambamba", freeVar = false)
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  def versionCommand = executable
  def versionRegex = """sambamba v(.*)""".r
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  override def versionExitcode = List(0, 1)
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}