Toucan.scala

/**
 * 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.pipelines.toucan

import java.io.File

import htsjdk.samtools.reference.FastaSequenceFile
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsIntersect, BedtoolsMerge }
import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweSamplesImport }
import nl.lumc.sasc.biopet.extensions.tools.{ GvcfToBed, VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Ln, VariantEffectPredictor }
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.broadinstitute.gatk.queue.QScript

/**
 * Pipeline to annotate a vcf file with VEP
 *
 * Created by ahbbollen on 15-1-15.
 */
class Toucan(val root: Configurable) extends QScript with BiopetQScript with SummaryQScript with Reference {
  def this() = this(null)

  @Input(doc = "Input VCF file", shortName = "Input", required = true)
  var inputVcf: File = _

  @Input(doc = "Input GVCF file", shortName = "gvcf", required = false)
  var inputGvcf: Option[File] = None

  def outputName = inputVcf.getName.stripSuffix(".vcf.gz")

  def outputVcf: File = (gonlVcfFile, exacVcfFile) match {
    case (Some(_), Some(_)) => new File(outputDir, s"$outputName.vep.normalized.gonl.exac.vcf.gz")
    case (Some(_), _)       => new File(outputDir, s"$outputName.vep.normalized.gonl.vcf.gz")
    case (_, Some(_))       => new File(outputDir, s"$outputName.vep.normalized.exac.vcf.gz")
    case _                  => new File(outputDir, s"$outputName.vep.normalized.vcf.gz")
  }

  lazy val minScatterGenomeSize: Long = config("min_scatter_genome_size", default = 75000000)

  lazy val enableScatter: Boolean = config("enable_scatter", default = {
    val ref = new FastaSequenceFile(referenceFasta(), true)
    val refLenght = ref.getSequenceDictionary.getReferenceLength
    ref.close()
    refLenght > minScatterGenomeSize
  })

  def sampleInfo: Map[String, Map[String, Any]] = root match {
    case m: MultiSampleQScript => m.samples.map { case (sampleId, sample) => sampleId -> sample.sampleTags }
    case null                  => VcfUtils.getSampleIds(inputVcf).map(x => x -> Map[String, Any]()).toMap
    case s: SampleLibraryTag   => s.sampleId.map(x => x -> Map[String, Any]()).toMap
    case _                     => throw new IllegalArgumentException("")
  }

  lazy val gonlVcfFile: Option[File] = config("gonl_vcf")
  lazy val exacVcfFile: Option[File] = config("exac_vcf")
  lazy val doVarda: Boolean = config("use_varda", default = false)

  def init(): Unit = {
    require(inputVcf != null, "No Input vcf given")
    inputFiles :+= new InputFile(inputVcf)
  }

  override def defaults = Map(
    "varianteffectpredictor" -> Map("everything" -> true, "failed" -> 1, "allow_non_variant" -> true)
  )

  def biopetScript(): Unit = {
    val useVcf: File = if (doVarda) {
      inputGvcf match {
        case Some(s) => varda(inputVcf, s)
        case _       => throw new IllegalArgumentException("You have not specified a GVCF file")
      }
    } else inputVcf

    if (enableScatter) {
      val outputVcfFiles = BedRecordList.fromReference(referenceFasta())
        .scatter(config("bin_size", default = 50000000))
        .allRecords.map { region =>

          val chunkName = s"${region.chr}-${region.start}-${region.end}"
          val chunkDir = new File(outputDir, "chunk" + File.separator + chunkName)
          chunkDir.mkdirs()
          val bedFile = new File(chunkDir, chunkName + ".bed")
          BedRecordList.fromList(List(region)).writeToFile(bedFile)
          bedFile.deleteOnExit()
          val sv = new SelectVariants(this)
          sv.variant = useVcf
          sv.out = new File(chunkDir, chunkName + ".vcf.gz")
          sv.intervals :+= bedFile
          sv.isIntermediate = true
          add(sv)

          runChunk(sv.out, chunkDir, chunkName)
        }

      val cv = new CatVariants(this)
      cv.variant = outputVcfFiles.toList
      cv.outputFile = outputVcf
      add(cv)
    } else runChunk(useVcf, outputDir, outputName)

    addSummaryJobs()
  }

  protected def runChunk(file: File, chunkDir: File, chunkName: String): File = {
    val vep = new VariantEffectPredictor(this)
    vep.input = file
    vep.output = new File(chunkDir, chunkName + ".vep.vcf")
    vep.isIntermediate = true
    add(vep)
    addSummarizable(vep, "variant_effect_predictor")

    val normalizer = new VepNormalizer(this)
    normalizer.inputVCF = vep.output
    normalizer.outputVcf = new File(chunkDir, chunkName + ".vep.normalized.vcf.gz")
    normalizer.isIntermediate = enableScatter || gonlVcfFile.isDefined || exacVcfFile.isDefined
    add(normalizer)

    var outputFile = normalizer.outputVcf

    gonlVcfFile match {
      case Some(gonlFile) =>
        val vcfWithVcf = new VcfWithVcf(this)
        vcfWithVcf.input = outputFile
        vcfWithVcf.secondaryVcf = gonlFile
        vcfWithVcf.output = swapExt(chunkDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
        vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
        vcfWithVcf.isIntermediate = enableScatter || exacVcfFile.isDefined
        add(vcfWithVcf)
        outputFile = vcfWithVcf.output
      case _ =>
    }

    exacVcfFile match {
      case Some(exacFile) =>
        val vcfWithVcf = new VcfWithVcf(this)
        vcfWithVcf.input = outputFile
        vcfWithVcf.secondaryVcf = exacFile
        vcfWithVcf.output = swapExt(chunkDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
        vcfWithVcf.fields ::= ("AF", "AF_exac", None)
        vcfWithVcf.isIntermediate = enableScatter
        add(vcfWithVcf)
        outputFile = vcfWithVcf.output
      case _ =>
    }

    outputFile
  }

  /**
   * Performs the varda import and activate for one sample
   *
   * @param sampleID the sampleID to be used
   * @param inputVcf the input VCF
   * @param gVCF the gVCF for coverage
   * @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
   * @return
   */
  def importAndActivateSample(sampleID: String, sampleGroups: List[String], inputVcf: File,
                              gVCF: File, annotation: ManweAnnotateVcf): ManweActivateAfterAnnotImport = {

    val minGQ: Int = config("minimum_genome_quality", default = 20, namespace = "manwe")
    val isPublic: Boolean = config("varda_is_public", default = true, namespace = "manwe")

    val bedTrack = new GvcfToBed(this)
    bedTrack.inputVcf = gVCF
    bedTrack.outputBed = swapExt(outputDir, gVCF, ".vcf.gz", s""".$sampleID.bed""")
    bedTrack.minQuality = minGQ
    bedTrack.isIntermediate = true
    bedTrack.sample = Some(sampleID)
    add(bedTrack)

    val mergedBed = new BedtoolsMerge(this)
    mergedBed.input = bedTrack.outputBed
    mergedBed.dist = 5
    mergedBed.output = swapExt(outputDir, bedTrack.outputBed, ".bed", ".merged.bed")
    add(mergedBed)

    val bgzippedBed = new Bgzip(this)
    bgzippedBed.input = List(mergedBed.output)
    bgzippedBed.output = swapExt(outputDir, mergedBed.output, ".bed", ".bed.gz")
    add(bgzippedBed)

    val singleVcf = new BcftoolsView(this)
    singleVcf.input = inputVcf
    singleVcf.output = swapExt(outputDir, inputVcf, ".vcf.gz", s""".$sampleID.vcf.gz""")
    singleVcf.samples = List(sampleID)
    singleVcf.minAC = Some(1)
    singleVcf.isIntermediate = true
    add(singleVcf)

    val intersected = new BedtoolsIntersect(this)
    intersected.input = singleVcf.output
    intersected.intersectFile = bgzippedBed.output
    intersected.output = swapExt(outputDir, singleVcf.output, ".vcf.gz", ".intersected.vcf")
    add(intersected)

    val bgzippedIntersect = new Bgzip(this)
    bgzippedIntersect.input = List(intersected.output)
    bgzippedIntersect.output = swapExt(outputDir, intersected.output, ".vcf", ".vcf.gz")
    add(bgzippedIntersect)

    val imported = new ManweSamplesImport(this)
    imported.vcfs = List(bgzippedIntersect.output)
    imported.beds = List(bgzippedBed.output)
    imported.name = Some(sampleID)
    imported.public = isPublic
    imported.group = sampleGroups
    imported.waitToComplete = false
    imported.isIntermediate = true
    imported.output = swapExt(outputDir, intersected.output, ".vcf.gz", ".manwe.import")
    add(imported)

    val active = new ManweActivateAfterAnnotImport(this, annotation, imported)
    active.output = swapExt(outputDir, imported.output, ".import", ".activated")
    add(active)
    active

  }

  /**
   * Perform varda analysis
   *
   * @param vcf input vcf
   * @param gVcf The gVCF to be used for coverage calculations
   * @return return vcf
   */
  def varda(vcf: File, gVcf: File): File = {

    val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), namespace = "manwe")

    val annotate = new ManweAnnotateVcf(this)
    annotate.vcf = vcf
    if (annotationQueries.nonEmpty) {
      annotate.queries = annotationQueries
    }
    annotate.waitToComplete = true
    annotate.output = swapExt(outputDir, vcf, ".vcf.gz", ".manwe.annot")
    annotate.isIntermediate = true
    add(annotate)

    val annotatedVcf = new ManweDownloadAfterAnnotate(this, annotate)
    annotatedVcf.output = swapExt(outputDir, annotate.output, ".manwe.annot", "manwe.annot.vcf.gz")
    add(annotatedVcf)

    val activates = sampleInfo map { x =>
      val sampleGroup = x._2.getOrElse("varda_group", Nil) match {
        case x: List[String] => x
        case Nil             => Nil
        case _               => throw new IllegalArgumentException("Sample tag 'varda_group' is not a list of strings")
      }
      importAndActivateSample(x._1, sampleGroup, vcf, gVcf, annotate)
    }

    val finalLn = new Ln(this)
    activates.foreach(x => finalLn.deps :+= x.output)
    finalLn.input = annotatedVcf.output
    finalLn.output = swapExt(outputDir, annotatedVcf.output, "manwe.annot.vcf.gz", ".varda_annotated.vcf.gz")
    finalLn.relative = true
    add(finalLn)

    finalLn.output
  }

  def summaryFile = new File(outputDir, "Toucan.summary.json")

  def summaryFiles = Map("input_vcf" -> inputVcf, "outputVcf" -> outputVcf)

  def summarySettings = Map()
}

object Toucan extends PipelineCommand