Adding delly mini-pipeline to yamsvc

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Delly.scala

+package nl.lumc.sasc.biopet.extensions.svcallers
+
+import java.io.File
+
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.BiopetQScript
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.Ln
+
+class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction {
+  executable = config("exe", default = "delly")
+
+  private lazy val versionexecutable: File = new File(executable)
+
+  override val defaultVmem = "8G"
+  override val defaultThreads = 1
+
+  override def versionCommand = versionexecutable.getAbsolutePath
+  override val versionRegex = """DELLY \(Version: (.*)\)""".r
+  override val versionExitcode = List(0, 1)
+
+  @Input(doc = "Input file (bam)")
+  var input: File = _
+
+  @Output(doc = "Delly VCF output")
+  var outputvcf: File = _
+
+  @Argument(doc = "What kind of analysis to run: DEL,DUP,INV,TRA")
+  var analysistype: String = _
+
+  def cmdLine = required(executable) +
+    "-t" + required(analysistype) +
+    "-o" + required(outputvcf) +
+    required(input)
+
+}
+
+class Delly(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Input file (bam)")
+  var input: File = _
+
+  @Argument(doc = "Work directory")
+  var workdir: String = _
+
+  @Output(doc = "Delly result VCF")
+  var outputvcf: File = _
+
+  var outputBaseName: String = _
+
+  // select the analysis types DEL,DUP,INV,TRA
+  var del: Boolean = config("DEL", default = false)
+  var dup: Boolean = config("DUP", default = false)
+  var inv: Boolean = config("INV", default = false)
+  var tra: Boolean = config("TRA", default = false)
+
+  override def init() {
+  }
+
+  def biopetScript() {
+    // write the pipeline here
+    logger.info("Configuring Delly pipeline")
+    var outputFiles: Map[String, File] = Map()
+    var vcfFiles: Map[String, File] = Map()
+
+    this.outputBaseName = workdir + input.getName.substring(0, input.getName.lastIndexOf(".bam"))
+    this.outputvcf = outputBaseName + ".delly.vcf"
+
+    /// 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 = outputBaseName + ".delly.del.vcf"
+      add(delly)
+      vcfFiles += ("DEL" -> delly.outputvcf)
+    }
+    if (dup) {
+      val delly = new DellyCaller(this)
+      delly.input = input
+      delly.analysistype = "DUP"
+      delly.outputvcf = outputBaseName + ".delly.dup.vcf"
+      add(delly)
+      vcfFiles += ("DUP" -> delly.outputvcf)
+    }
+    if (inv) {
+      val delly = new DellyCaller(this)
+      delly.input = input
+      delly.analysistype = "INV"
+      delly.outputvcf = outputBaseName + ".delly.inv.vcf"
+      add(delly)
+      vcfFiles += ("INV" -> delly.outputvcf)
+    }
+    if (tra) {
+      val delly = new DellyCaller(this)
+      delly.input = input
+      delly.analysistype = "TRA"
+      delly.outputvcf = outputBaseName + ".delly.tra.vcf"
+      //      vcfFiles += ("TRA" -> delly.outputvcf)
+      add(delly)
+    }
+    // we need to merge the vcf's
+    var finalVCF = if (vcfFiles.size > 1) {
+      // do merging
+      // CatVariants is a $org.broadinstitute.gatk.utils.commandline.CommandLineProgram$;
+      val variants = new CatVariants()
+      variants.jobResourceRequests :+= "h_vmem=4G"
+      variants.nCoresRequest = 1
+      variants.memoryLimit = Option(2.0)
+      variants.variant = vcfFiles.values.toList
+      variants.reference = config("reference")
+      variants.outputFile = this.outputvcf
+      // add the job
+      add(variants)
+    } else {
+      // TODO: pretify this
+      val ln = Ln(this, vcfFiles.head._2, this.outputvcf, relative = true)
+      add(ln)
+      ln.out
+    }
+
+    outputFiles += ("vcf" -> this.outputvcf)
+  }
+
+  private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".delly.vcf"
+}
+
+object Delly extends PipelineCommand {
+  override val pipeline = "/nl/lumc/sasc/biopet/extensions/svcallers/Delly/Delly.class"
+
+  def apply(root: Configurable, input: File, runDir: String): Delly = {
+    val dellypipeline = new Delly(root)
+    dellypipeline.input = input
+    dellypipeline.workdir = runDir
+    dellypipeline.init
+    dellypipeline.biopetScript
+    return dellypipeline
+  }
+
+}
\ No newline at end of file

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala

@@ -11,7 +11,7 @@ import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge }
 import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
-import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Clever }
+import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Clever, Delly }
 
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 
@@ -108,6 +108,14 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
     val bd_vcf = Ln(this, breakdancer.outputvcf, svcallingDir + sampleID + ".breakdancer.vcf", relative = true)
     add(bd_vcf)
 
+    val dellyDir = svcallingDir + sampleID + ".delly/"
+    val delly = Delly(this, bamFile, dellyDir)
+    sampleOutput.vcf += ("delly" -> List(delly.outputvcf))
+    addAll(delly.functions)
+
+    val delly_vcf = Ln(this, delly.outputvcf, svcallingDir + sampleID + ".delly.vcf", relative = true)
+    add(delly_vcf)
+
     // for pindel we should use per library config collected into one config file
     //    val pindelDir = svcallingDir + sampleID + ".pindel/"
     //    val pindel = Pindel(this, bamFile, this.reference, pindelDir)