Move mini pipeline delly

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Delly.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.shiva
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
-import nl.lumc.sasc.biopet.extensions.Ln
-import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
-
-import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.QScript
-
-class Delly(val root: Configurable) extends QScript with Reference with SummaryQScript {
-  def this() = this(null)
-
-  @Input(doc = "Input file (bam)")
-  var input: File = _
-
-  var workDir: File = _
-
-  @Output(doc = "Delly result VCF")
-  var outputVcf: File = _
-
-  this.inputFiles
-
-  var outputName: String = _
-
-  // select the analysis types DEL,DUP,INV,TRA
-  var del: Boolean = config("DEL", default = true)
-  var dup: Boolean = config("DUP", default = true)
-  var inv: Boolean = config("INV", default = true)
-  var tra: Boolean = config("TRA", default = true)
-
-  override def init(): Unit = {
-    if (outputName == null) outputName = input.getName.stripSuffix(".bam")
-    if (outputVcf == null) outputVcf = new File(workDir, outputName + ".delly.vcf")
-  }
-
-  override def summaryFile: File = new File(workDir, "Delly.summary.json")
-
-  override def summaryFiles: Map[String, File] = Map.empty ++
-    Map("input" -> input) ++
-    Map("outputVCF" -> outputVcf)
-
-  override def summarySettings = {
-    Map(
-      "workDir" -> workDir,
-      "outputName" -> outputName,
-      "del" -> del,
-      "dup" -> dup,
-      "inv" -> inv,
-      "tra" -> tra
-    )
-  }
-
-  def biopetScript() {
-    // write the pipeline here
-    logger.info("Configuring Delly pipeline")
-
-    var outputFiles: Map[String, File] = Map()
-    var vcfFiles: Map[String, File] = Map()
-
-    /// start delly and then copy the vcf into the root directory "<sample>.delly/"
-    if (del) {
-      val delly = new DellyCaller(this)
-      delly.input = input
-      delly.analysistype = "DEL"
-      delly.outputvcf = new File(workDir, outputName + ".delly.del.vcf")
-      add(delly)
-      vcfFiles += ("DEL" -> delly.outputvcf)
-    }
-    if (dup) {
-      val delly = new DellyCaller(this)
-      delly.input = input
-      delly.analysistype = "DUP"
-      delly.outputvcf = new File(workDir, outputName + ".delly.dup.vcf")
-      add(delly)
-      vcfFiles += ("DUP" -> delly.outputvcf)
-    }
-    if (inv) {
-      val delly = new DellyCaller(this)
-      delly.input = input
-      delly.analysistype = "INV"
-      delly.outputvcf = new File(workDir, outputName + ".delly.inv.vcf")
-      add(delly)
-      vcfFiles += ("INV" -> delly.outputvcf)
-    }
-    if (tra) {
-      val delly = new DellyCaller(this)
-      delly.input = input
-      delly.analysistype = "TRA"
-      delly.outputvcf = new File(workDir, outputName + ".delly.tra.vcf")
-      //      vcfFiles += ("TRA" -> delly.outputvcf)
-      add(delly)
-    }
-    // we need to merge the vcf's
-    val finalVCF = if (vcfFiles.size > 1) {
-      // do merging
-      val variants = new CatVariants(this)
-      variants.inputFiles = vcfFiles.values.toList
-      variants.outputFile = this.outputVcf
-      //      variants.reference = referenceFasta()
-      // add the job
-      add(variants)
-      Some(variants.outputFile)
-    } else if (vcfFiles.size == 1) {
-      // TODO: pretify this
-      val ln = Ln(this, vcfFiles.head._2, this.outputVcf, relative = true)
-      //add(ln)
-      Some(ln.output)
-    } else None
-
-    finalVCF.foreach(file => outputFiles += ("vcf" -> file))
-  }
-}
-
-object Delly extends PipelineCommand {
-  def apply(root: Configurable, input: File, workDir: File): Delly = {
-    val dellyPipeline = new Delly(root)
-    dellyPipeline.input = input
-    dellyPipeline.workDir = workDir
-    dellyPipeline.init()
-    dellyPipeline.biopetScript()
-    dellyPipeline
-  }
-
-}
\ No newline at end of file

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.delly.Delly
+import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
+import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caler delly */
 class Delly(val root: Configurable) extends SvCaller {
   def name = "delly"
 
+  val del: Boolean = config("DEL", default = true)
+  val dup: Boolean = config("DUP", default = true)
+  val inv: Boolean = config("INV", default = true)
+  val tra: Boolean = config("TRA", default = true)
+
   def biopetScript() {
-    //TODO: Move mini delly pipeline to here
     for ((sample, bamFile) <- inputBams) {
       val dellyDir = new File(outputDir, sample)
-      val delly = Delly(this, bamFile, dellyDir)
-      delly.outputName = sample
-      addAll(delly.functions)
+
+      val catVariants = new CatVariants(this)
+      catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf.gz")
+
+      /// start delly and then copy the vcf into the root directory "<sample>.delly/"
+      if (del) {
+        val delly = new DellyCaller(this)
+        delly.input = bamFile
+        delly.analysistype = "DEL"
+        delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
+        add(delly)
+        catVariants.inputFiles :+= delly.outputvcf
+      }
+      if (dup) {
+        val delly = new DellyCaller(this)
+        delly.input = bamFile
+        delly.analysistype = "DUP"
+        delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
+        add(delly)
+        catVariants.inputFiles :+= delly.outputvcf
+      }
+      if (inv) {
+        val delly = new DellyCaller(this)
+        delly.input = bamFile
+        delly.analysistype = "INV"
+        delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
+        add(delly)
+        catVariants.inputFiles :+= delly.outputvcf
+      }
+      if (tra) {
+        val delly = new DellyCaller(this)
+        delly.input = bamFile
+        delly.analysistype = "TRA"
+        delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
+        catVariants.inputFiles :+= delly.outputvcf
+        add(delly)
+      }
+
+      add(catVariants)
     }
   }
 }