varda in Toucan

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GvcfToBed.scala

+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
+
+/**
+ * Created by ahbbollen on 13-10-15.
+ */
+class GvcfToBed (val root: Configurable) extends ToolCommandFuntion {
+  def toolObject = nl.lumc.sasc.biopet.tools.GvcfToBed
+
+  @Input(doc = "input vcf")
+  var inputVcf: File = _
+
+  @Output(doc = "output bed")
+  var outputBed: File = _
+
+  @Argument(doc = "sample")
+  var sample: Option[String] = None
+
+  @Argument(doc = "minquality")
+  var minQuality: Int = 0
+
+  @Argument(doc = "inverse")
+  var inverse: Boolean = false
+
+  override def defaultCoreMemory = 4.0
+
+  override def cmdLine = {
+    super.cmdLine +
+    required("-I", inputVcf) +
+    required("-O", outputBed) +
+    optional("-S", sample) +
+    optional("--minGenomeQuality", minQuality) +
+    conditional(inverse, "--inverted")
+  }
+
+}

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala

@@ -34,6 +34,7 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
   var minTotalDepth: Option[Int] = config("min_total_depth")
   var minAlternateDepth: Option[Int] = config("min_alternate_depth")
   var minSamplesPass: Option[Int] = config("min_samples_pass")
+  var minGenomeQuality: Option[Int] = config("min_genome_quality")
   var filterRefCalls: Boolean = config("filter_ref_calls", default = false)
 
   override def defaultCoreMemory = 3.0
@@ -45,5 +46,6 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
     optional("--minTotalDepth", minTotalDepth) +
     optional("--minAlternateDepth", minAlternateDepth) +
     optional("--minSamplesPass", minSamplesPass) +
+    optional("--minGenomeQuality", minGenomeQuality) +
     conditional(filterRefCalls, "--filterRefCalls")
 }

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -15,11 +15,13 @@
  */
 package nl.lumc.sasc.biopet.pipelines.toucan
 
+import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
+import nl.lumc.sasc.biopet.extensions.manwe.{ManweSamplesImport, ManweAnnotateVcf, ManweDataSourcesAnnotate}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
-import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
-import nl.lumc.sasc.biopet.extensions.tools.{ VcfWithVcf, VepNormalizer }
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.extensions.{Ln, Gzip, VariantEffectPredictor}
+import nl.lumc.sasc.biopet.extensions.tools.{GvcfToBed, VcfFilter, VcfWithVcf, VepNormalizer}
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 
@@ -28,20 +30,26 @@ import org.broadinstitute.gatk.queue.QScript
  *
  * Created by ahbbollen on 15-1-15.
  */
-class Toucan(val root: Configurable) extends QScript with BiopetQScript with SummaryQScript with Reference {
+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 = _
 
+  var sampleIds: List[String] = Nil
   def init(): Unit = {
     inputFiles :+= new InputFile(inputVCF)
+    sampleIds = root match {
+      case m: MultiSampleQScript => m.samples.keys.toList
+      case null => Nil //TODO: get names from vcf header
+      case s: SampleLibraryTag => s.sampleId.toList
+      case _ => throw new IllegalArgumentException("You don't have any samples")
+    }
   }
 
   override def defaults = Map(
     "varianteffectpredictor" -> Map("everything" -> true)
   )
-
   //defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
 
   def biopetScript(): Unit = {
@@ -87,6 +95,93 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     }
   }
 
+  /**
+   * Perform varda analysis
+   * @param vcf input vcf
+   * @return return vcf
+   */
+  def varda(vcf: File): File = {
+    val splits = sampleIds.map(x => {
+      val view = new BcftoolsView(this)
+      view.input = vcf
+      view.output = swapExt(vcf, ".vcf.gz", s"$x.vcf.gz")
+      view.samples = List(x)
+      view.minAC = Some(1)
+      add(view)
+      view
+    })
+
+    val minGQ = config("minimumGenomeQuality", default = 20)
+    val vardaConfig: Option[File] = config("vardaConfig") // TODO: create on the fly
+    val annotationQueries: List[String] = config("annotationQueries")
+    val isPublic: Boolean = config("vardaIsPublic")
+
+    val filteredVcfs = splits.map(x => {
+      val filter = new VcfFilter(this)
+      filter.inputVcf = x.output
+      filter.outputVcf = swapExt(x.output, ".vcf.gz", ".filtered.vcf.gz")
+      filter.minGenomeQuality = minGQ
+      add(filter)
+      filter
+    })
+
+    val bedTracks = filteredVcfs.map(x => {
+      val bed = new GvcfToBed(this)
+      bed.inputVcf = x.outputVcf
+      bed.outputBed = swapExt(x.outputVcf, ".vcf.gz", ".bed")
+      add(bed)
+      bed
+    })
+
+    val zippedBedTracks = bedTracks.map(x => {
+      val gzip = new Gzip(this)
+      gzip.input = List(x.outputBed)
+      gzip.output = swapExt(x.outputBed, ".bed", ".bed.gz")
+      add(gzip)
+      gzip
+    })
+
+    val annotate = new ManweAnnotateVcf(this)
+    annotate.vcf = vcf
+    annotate.manweConfig = vardaConfig
+    annotate.queries = annotationQueries
+    annotate.waitToComplete = true
+    annotate.output = swapExt(vcf, ".vcf.gz", ".tmp.annot")
+    add(annotate)
+
+    val annotatedVcf = new ManweDownloadAfterAnnotate(this, annotate)
+    annotatedVcf.output = swapExt(annotate.output, ".tmp.annot", "tmp.annot.vcf.gz")
+
+    val imports = for (
+      (sample: String, bed, vcf) <- (sampleIds, bedTracks, filteredVcfs).zipped
+    ) yield {
+        val importing = new ManweSamplesImport(this)
+        importing.beds = List(bed.outputBed)
+        importing.vcfs = List(vcf.outputVcf)
+        importing.name = Some(sample)
+        importing.waitToComplete = true
+        importing.output = swapExt(vcf.outputVcf, ".vcf.gz", ".tmp.import")
+        importing.public = isPublic
+        importing.manweConfig = vardaConfig
+        importing
+      }
+
+    val activates = imports.map(x => {
+      val active = new ManweActivateAfterAnnotImport(this, annotate, x)
+      active.manweConfig = vardaConfig
+      active.output = swapExt(x.output, ".tmp.import", ".tmp.activated")
+      active
+    })
+
+    val finalLn = new Ln(this)
+    activates.foreach(x => finalLn.deps :+= x)
+    finalLn.input = annotatedVcf.output
+    finalLn.output = swapExt(annotatedVcf.output, "tmp.annot.vcf.gz", ".varda_annotated.vcf.gz")
+    finalLn.relative = true
+
+    finalLn.output
+  }
+
   def summaryFile = new File(outputDir, "Toucan.summary.json")
 
   def summaryFiles = Map()