Split sv callers into separated classes

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

@@ -17,9 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
-import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
-import nl.lumc.sasc.biopet.extensions.delly.Delly
+import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{Delly, Breakdancer, Clever, SvCaller}
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
@@ -59,68 +57,13 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
     require(inputBams.nonEmpty, "No input bams found")
     require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
 
-    callers.foreach(_.addJobs())
+    callers.foreach(add)
 
     addSummaryJobs()
   }
 
   /** Will generate all available variantcallers */
-  protected def callersList: List[SvCaller] = List(new Breakdancer, new Clever, new Delly)
-
-  /** General trait for a variantcaller mode */
-  trait SvCaller {
-    /** Name of mode, this should also be used in the config */
-    val name: String
-
-    /** Output dir for this mode */
-    def outputDir = new File(qscript.outputDir, name)
-
-    /** This should add the variantcaller jobs */
-    def addJobs()
-  }
-
-  /** default mode of freebayes */
-  class Breakdancer extends SvCaller {
-    val name = "breakdancer"
-
-    def addJobs() {
-      //TODO: move minipipeline of breakdancer to here
-      for ((sample, bamFile) <- inputBams) {
-        val breakdancerDir = new File(outputDir, sample)
-        val breakdancer = Breakdancer(qscript, bamFile, breakdancerDir)
-        addAll(breakdancer.functions)
-      }
-    }
-  }
-
-  /** default mode of bcftools */
-  class Clever extends SvCaller {
-    val name = "clever"
-
-    def addJobs() {
-      //TODO: check double directories
-      for ((sample, bamFile) <- inputBams) {
-        val cleverDir = new File(outputDir, sample)
-        val clever = CleverCaller(qscript, bamFile, cleverDir)
-        add(clever)
-      }
-    }
-  }
-
-  /** Makes a vcf file from a mpileup without statistics */
-  class Delly extends SvCaller {
-    val name = "delly"
-
-    def addJobs() {
-      //TODO: Move mini delly pipeline to here
-      for ((sample, bamFile) <- inputBams) {
-        val dellyDir = new File(outputDir, sample)
-        val delly = Delly(qscript, bamFile, dellyDir)
-        delly.outputName = sample
-        addAll(delly.functions)
-      }
-    }
-  }
+  protected def callersList: List[SvCaller] = List(new Breakdancer(this), new Clever(this), new Delly(this))
 
   /** Location of summary file */
   def summaryFile = new File(outputDir, "ShivaSvCalling.summary.json")

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

+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript}
+import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
+import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
+import nl.lumc.sasc.biopet.extensions.delly.Delly
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+  * Created by pjvanthof on 23/11/15.
+  */
+trait SvCaller extends QScript with BiopetQScript with Reference {
+
+  /** Name of mode, this should also be used in the config */
+  def name: String
+
+  var namePrefix: String = _
+
+  var inputBams: Map[String, File] = _
+
+  def init() = {}
+}
+
+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)
+    }
+  }
+}
+
+/** default mode of bcftools */
+class Clever(val root: Configurable) extends SvCaller {
+  def name = "clever"
+
+  def biopetScript() {
+    //TODO: check double directories
+    for ((sample, bamFile) <- inputBams) {
+      val cleverDir = new File(outputDir, sample)
+      val clever = CleverCaller(this, bamFile, cleverDir)
+      add(clever)
+    }
+  }
+}
+
+/** Makes a vcf file from a mpileup without statistics */
+class Delly(val root: Configurable) extends SvCaller {
+  def name = "delly"
+
+  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)
+    }
+  }
+}

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala

@@ -23,9 +23,6 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
   /** Prio from the config */
   lazy val prio: Int = config("prio_" + name, default = defaultPrio)
 
-  /** This should add the variantcaller jobs */
-  def script
-
   /** Final output file of this mode */
   def outputFile: File = new File(outputDir, namePrefix + s".$name.vcf.gz")
 }