Convert breakdancer to sub pipeline of shiva

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.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.extensions.breakdancer
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
-
-/// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
-class Breakdancer(val root: Configurable) extends QScript with BiopetQScript with Reference {
-  def this() = this(null)
-
-  @Input(doc = "Input file (bam)")
-  var input: File = _
-
-  @Argument(doc = "Work directory")
-  var workDir: File = _
-
-  var deps: List[File] = Nil
-
-  @Output(doc = "Breakdancer config")
-  lazy val configfile: File = {
-    new File(workDir, input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.cfg")
-  }
-  @Output(doc = "Breakdancer raw output")
-  lazy val outputraw: File = {
-    new File(workDir, input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.tsv")
-  }
-  @Output(doc = "Breakdancer VCF output")
-  lazy val outputvcf: File = {
-    new File(workDir, input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.vcf")
-  }
-
-  override def init(): Unit = {
-  }
-
-  def biopetScript() {
-    // read config and set all parameters for the pipeline
-    logger.info("Starting Breakdancer configuration")
-
-    val bdcfg = BreakdancerConfig(this, input, this.configfile)
-    bdcfg.deps = this.deps
-    outputFiles += ("cfg" -> bdcfg.output)
-    add(bdcfg)
-
-    val breakdancer = BreakdancerCaller(this, bdcfg.output, this.outputraw)
-    add(breakdancer)
-    outputFiles += ("tsv" -> breakdancer.output)
-
-    val bdvcf = BreakdancerVCF(this, breakdancer.output, this.outputvcf)
-    add(bdvcf)
-    outputFiles += ("vcf" -> bdvcf.output)
-  }
-}
-
-object Breakdancer extends PipelineCommand {
-  def apply(root: Configurable, input: File, runDir: File): Breakdancer = {
-    val breakdancer = new Breakdancer(root)
-    breakdancer.input = input
-    breakdancer.workDir = runDir
-    breakdancer.init()
-    breakdancer.biopetScript()
-    breakdancer
-  }
-}
\ No newline at end of file

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

 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
+import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerVCF, BreakdancerCaller, BreakdancerConfig}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caler Breakdancer */
@@ -8,11 +8,16 @@ class Breakdancer(val root: Configurable) extends SvCaller {
   def name = "breakdancer"
 
   def biopetScript() {
-    //TODO: move minipipeline of breakdancer to here
     for ((sample, bamFile) <- inputBams) {
-      val breakdancerDir = new File(outputDir, sample)
-      val breakdancer = Breakdancer(this, bamFile, breakdancerDir)
-      addAll(breakdancer.functions)
+      val breakdancerSampleDir = new File(outputDir, sample)
+
+      // read config and set all parameters for the pipeline
+      logger.debug("Starting Breakdancer configuration")
+
+      val bdcfg = BreakdancerConfig(this, bamFile, new File(breakdancerSampleDir, sample + ".breakdancer.cfg"))
+      val breakdancer = BreakdancerCaller(this, bdcfg.output, new File(breakdancerSampleDir, sample + ".breakdancer.tsv"))
+      val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"))
+      add(bdcfg, breakdancer, bdvcf)
     }
   }
 }