Removing method

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/somatic/MuTect2.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.somatic
 
 import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
 import nl.lumc.sasc.biopet.extensions.{Awk, Tabix, gatk}
-import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.{ConfigValue, Configurable}
 
 class MuTect2(val parent: Configurable) extends SomaticVariantCaller {
 
@@ -12,50 +12,53 @@ class MuTect2(val parent: Configurable) extends SomaticVariantCaller {
 
   // currently not relevant, at the moment only one somatic variant caller exists in Biopet
   // and results from this won't be merged together with the results from other methods
-  def defaultPrio = -1
+  def defaultPrio: Int = -1
 
-  val runConEst = config("run_contest", default = false)
+  lazy val runConEst: Boolean = config("run_contest", default = false)
 
   def biopetScript(): Unit = {
 
-    for (pair <- tnPairs)
-      addJobsForPair(pair,
-                     new File(outputDir, s"${pair.tumorSample}-${pair.normalSample}.$name.vcf.gz"))
-  }
+    val outputFiles = for (pair <- tnPairs) yield {
 
-  def addJobsForPair(pair: TumorNormalPair, outFile: File): Unit = {
-    val muTect2 = {
-      gatk.MuTect2(this, inputBams(pair.tumorSample), inputBams(pair.normalSample), outFile)
-    }
+      val outputFile = new File(outputDir, s"${pair.tumorSample}-${pair.normalSample}.$name.vcf.gz")
 
-    if (runConEst) {
-      val namePrefix = outFile.getAbsolutePath.stripSuffix(".vcf.gz")
-      val contEstOutput: File = new File(s"$namePrefix.contamination.txt")
-      val contEst = gatk.ContEst(this,
-                                 inputBams(pair.tumorSample),
-                                 inputBams(pair.normalSample),
-                                 contEstOutput)
-      add(contEst)
-
-      val contaminationPerSample: File = new File(s"$namePrefix.contamination.short.txt")
-      val awk: Awk = Awk(this, "BEGIN{OFS=\"\\t\"}{if($1 != \"name\") print $1,$4;}")
-      awk.input = contEstOutput
-      add(awk > contaminationPerSample)
-
-      muTect2.contaminationFile = Some(contaminationPerSample)
-    }
+      val muTect2 = {
+        gatk.MuTect2(this, inputBams(pair.tumorSample), inputBams(pair.normalSample), outputFile)
+      }
 
-    if (inputBqsrFiles.contains(pair.tumorSample) && inputBqsrFiles.contains(pair.normalSample)) {
-      val gather = new BqsrGather()
-      gather.inputBqsrFiles =
-        List(inputBqsrFiles(pair.tumorSample), inputBqsrFiles(pair.normalSample))
-      gather.outputBqsrFile = new File(swapExt(outFile, "vcf.gz", "bqsr.merge"))
-      add(gather)
+      if (runConEst) {
+        val namePrefix = outputFile.getAbsolutePath.stripSuffix(".vcf.gz")
+        val contEstOutput: File = new File(s"$namePrefix.contamination.txt")
+        val contEst = gatk.ContEst(this,
+          inputBams(pair.tumorSample),
+          inputBams(pair.normalSample),
+          contEstOutput)
+        add(contEst)
 
-      muTect2.BQSR = Some(gather.outputBqsrFile)
-    }
+        val contaminationPerSample: File = new File(s"$namePrefix.contamination.short.txt")
+        val awk: Awk = Awk(this, "BEGIN{OFS=\"\\t\"}{if($1 != \"name\") print $1,$4;}")
+        awk.input = contEstOutput
+        add(awk > contaminationPerSample)
+
+        muTect2.contaminationFile = Some(contaminationPerSample)
+      }
 
-    add(muTect2)
-    add(Tabix(this, outFile))
+      if (inputBqsrFiles.contains(pair.tumorSample) && inputBqsrFiles.contains(pair.normalSample)) {
+        val gather = new BqsrGather()
+        gather.inputBqsrFiles =
+          List(inputBqsrFiles(pair.tumorSample), inputBqsrFiles(pair.normalSample))
+        gather.outputBqsrFile = new File(swapExt(outputFile, "vcf.gz", "bqsr.merge"))
+        add(gather)
+
+        muTect2.BQSR = Some(gather.outputBqsrFile)
+      }
+
+      // TODO: Add name change
+
+      add(muTect2)
+      add(Tabix(this, outputFile))
+
+      outputFile
+    }
   }
 }