Update breakdancer

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala

@@ -18,38 +18,36 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+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 {
+class Breakdancer(val root: Configurable) extends QScript with BiopetQScript with Reference {
   def this() = this(null)
 
   @Input(doc = "Input file (bam)")
   var input: File = _
 
-  @Input(doc = "Reference Fasta file")
-  var reference: File = _
-
   @Argument(doc = "Work directory")
-  var workdir: String = _
+  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")
+    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")
+    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")
+    new File(workDir, input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.vcf")
   }
 
-  override def init() {
+  override def init(): Unit = {
+    
   }
 
   def biopetScript() {
@@ -72,11 +70,10 @@ class Breakdancer(val root: Configurable) extends QScript with BiopetQScript {
 }
 
 object Breakdancer extends PipelineCommand {
-  def apply(root: Configurable, input: File, reference: File, runDir: String): Breakdancer = {
+  def apply(root: Configurable, input: File, runDir: File): Breakdancer = {
     val breakdancer = new Breakdancer(root)
     breakdancer.input = input
-    breakdancer.reference = reference
-    breakdancer.workdir = runDir
+    breakdancer.workDir = runDir
     breakdancer.init()
     breakdancer.biopetScript()
     breakdancer

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

@@ -24,7 +24,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
   var reference: File = _
 
   @Argument(doc = "Work directory")
-  var workdir: String = _
+  var workDir: String = _
 
   var cwd: String = _
 
@@ -35,7 +35,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Output(doc = "Clever raw output")
   lazy val outputraw: File = {
-    new File(workdir + "predictions.raw.txt")
+    new File(workDir + "predictions.raw.txt")
   }
 
   //  var T: Option[Int] = config("T", default = defaultThreads)
@@ -46,7 +46,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
   var r: Boolean = config("r", default = false) // take read groups into account
 
   override def beforeCmd() {
-    if (workdir == null) throw new Exception("Clever :: Workdirectory is not defined")
+    if (workDir == null) throw new Exception("Clever :: Workdirectory is not defined")
     //    if (input.getName.endsWith(".sort.bam")) sorted = true
   }
 
@@ -58,9 +58,9 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
     conditional(a, "-a") +
     conditional(k, "-k") +
     conditional(r, "-r") +
-    required(this.input) +
-    required(this.reference) +
-    required(this.workdir)
+    required(input) +
+    required(reference) +
+    required(workDir)
 }
 
 object CleverCaller {
@@ -69,7 +69,7 @@ object CleverCaller {
     clever.input = input
     clever.reference = reference
     clever.cwd = svDir
-    clever.workdir = runDir
+    clever.workDir = runDir
     clever
   }
 }
\ No newline at end of file

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

@@ -19,7 +19,7 @@ import java.io.File
 
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{PipelineCommand, BiopetQScript, Reference, SampleLibraryTag}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript, 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
@@ -41,7 +41,7 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
 
   protected def addBamFile(file: File, sampleId: Option[String] = None): Unit = {
     sampleId match {
-      case Some(sample) => inputBams += sample -> file
+      case Some(sample)        => inputBams += sample -> file
       case _ if !file.exists() => throw new IllegalArgumentException("Bam file does not exits: " + file)
       case _ => {
         val inputSam = SamReaderFactory.makeDefault.open(file)
@@ -68,7 +68,7 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
         BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
     }
 
-    val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)
+    val callers = callersList.filter(x => configCallers.contains(x.name))
 
     require(inputBams.nonEmpty, "No input bams found")
     require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
@@ -99,7 +99,7 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
       //TODO: move minipipeline of breakdancer to here
       for ((sample, bamFile) <- inputBams) {
         val breakdancerDir = new File(outputDir, sample)
-        val breakdancer = Breakdancer(qscript, bamFile, qscript.reference, breakdancerDir)
+        val breakdancer = Breakdancer(qscript, bamFile, breakdancerDir)
         addAll(breakdancer.functions)
       }
     }
@@ -112,7 +112,7 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
     def addJobs() {
       //TODO: check double directories
       for ((sample, bamFile) <- inputBams) {
-        val cleverDir = new File(outputDir, sampleId)
+        val cleverDir = new File(outputDir, sample)
         val clever = CleverCaller(qscript, bamFile, qscript.reference, cleverDir, cleverDir)
         add(clever)
       }
@@ -126,7 +126,7 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
     def addJobs() {
       //TODO: Move mini delly pipeline to here
       for ((sample, bamFile) <- inputBams) {
-        val dellyDir = new File(outputDir, sampleId)
+        val dellyDir = new File(outputDir, sample)
         val delly = Delly(qscript, bamFile, dellyDir)
         addAll(delly.functions)
       }
@@ -142,7 +142,8 @@ class ShivaSvCalling extends SummaryQScript with SampleLibraryTag with Reference
   /** Files for the summary */
   def summaryFiles: Map[String, File] = {
     val callers: Set[String] = config("sv_callers")
-    callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
+    //callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
+    Map()
   }
 }