MultiSampleQScript.scala 5.99 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.core

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import java.io.File

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import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
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import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
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import org.broadinstitute.gatk.utils.commandline.Argument
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/** This trait creates a structured way of use multisample pipelines */
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trait MultiSampleQScript extends SummaryQScript {
  qscript =>

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  @Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
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  private[core] val onlySamples: List[String] = Nil
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  require(globalConfig.map.contains("samples"), "No Samples found in config")
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  /** Sample class with basic functions build in */
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  abstract class AbstractSample(val sampleId: String) extends Summarizable {
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    /** Overrules config of qscript with default sample */
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    val config = new ConfigFunctions(defaultSample = sampleId)
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    /** Library class with basic functions build in */
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    abstract class AbstractLibrary(val libId: String) extends Summarizable {
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      /** Overrules config of qscript with default sample and default library */
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      val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
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      /** Name overules the one from qscript */
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      def addSummarizable(summarizable: Summarizable, name: String): Unit = {
        qscript.addSummarizable(summarizable, name, Some(sampleId), Some(libId))
      }

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      /** Adds the library jobs */
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      final def addAndTrackJobs(): Unit = {
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        currentSample = Some(sampleId)
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        currentLib = Some(libId)
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        addJobs()
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        qscript.addSummarizable(this, "pipeline", Some(sampleId), Some(libId))
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        currentLib = None
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        currentSample = None
      }

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      /** Creates a library file with given suffix */
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      def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libId + suffix)
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      /** Returns library directory */
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      def libDir = new File(sampleDir, "lib_" + libId)
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      /** Function that add library jobs */
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      protected def addJobs()
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    }
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    /** Library type, need implementation in pipeline */
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    type Library <: AbstractLibrary
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    /** Stores all libraries */
    val libraries: Map[String, Library] = libIds.map(id => id -> makeLibrary(id)).toMap
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    /**
     * Factory method for Library class
     * @param id SampleId
     * @return Sample class
     */
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    def makeLibrary(id: String): Library
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    /** returns a set with library names */
    protected def libIds: Set[String] = {
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      ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
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    }
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    /** Name overules the one from qscript */
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    def addSummarizable(summarizable: Summarizable, name: String): Unit = {
      qscript.addSummarizable(summarizable, name, Some(sampleId))
    }

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    /** Adds sample jobs */
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    final def addAndTrackJobs(): Unit = {
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      if (sampleRegex.findFirstIn(sampleId) == None)
        Logging.addError(s"Sample '$sampleId' contains illegal chars")
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      currentSample = Some(sampleId)
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      addJobs()
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      qscript.addSummarizable(this, "pipeline", Some(sampleId))
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      currentSample = None
    }
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    /** Function to add sample jobs */
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    protected def addJobs()
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    /** function add all libraries in one call */
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    protected final def addPerLibJobs(): Unit = {
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      for ((libId, library) <- libraries) {
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        library.addAndTrackJobs()
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      }
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    }

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    /** Creates a sample file with given suffix */
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    def createFile(suffix: String) = new File(sampleDir, sampleId + suffix)

    /** Returns sample directory */
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    def sampleDir = new File(outputDir, "samples" + File.separator + sampleId)
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  }

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  /** Sample type, need implementation in pipeline */
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  type Sample <: AbstractSample

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  /**
   * Factory method for Sample class
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   * @param id SampleId
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   * @return Sample class
   */
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  def makeSample(id: String): Sample
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  /** Stores all samples */
  val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
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  /** Returns a list of all sampleIDs */
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  protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
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  protected lazy val sampleRegex = """^[a-zA-Z0-9-_]+$""".r

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  /** Runs addAndTrackJobs method for each sample */
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  final def addSamplesJobs() {
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    if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
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      samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
      addMultiSampleJobs()
    } else onlySamples.foreach(sampleId => samples.get(sampleId) match {
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      case Some(sample) => sample.addAndTrackJobs()
      case None         => logger.warn("sampleId '" + sampleId + "' not found")
    })
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  }

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  /**
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   * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
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   */
  def addMultiSampleJobs()

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  /** Stores sample state */
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  private var currentSample: Option[String] = None

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  /** Stores library state */
  private var currentLib: Option[String] = None

  /** Prefix full path with sample and library for jobs that's are created in current state */
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  override def configFullPath: List[String] = {
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    val sample = currentSample match {
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      case Some(s) => "samples" :: s :: Nil
      case _       => Nil
    }
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    val lib = currentLib match {
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      case Some(l) => "libraries" :: l :: Nil
      case _       => Nil
    }
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    sample ::: lib ::: super.configFullPath
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  }
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}