Fix code style warnings

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -18,6 +18,6 @@ object AnalyzeCovariates {
     ac.before = before
     ac.after = after
     ac.plots = plots
-    return ac
+    ac
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -12,8 +12,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
   scatterCount = config("scattercount", default = 0)
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
 
     nt = Option(getThreads(3))
     memoryLimit = Option(nt.getOrElse(1) * 2)
@@ -37,6 +37,6 @@ object ApplyRecalibration {
     ar.recal_file = recal_file
     ar.tranches_file = tranches_file
     ar.out = output
-    return ar
+    ar
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -20,7 +20,7 @@ object BaseRecalibrator {
     val br = new BaseRecalibrator(root)
     br.input_file :+= input
     br.out = output
-    br.beforeGraph
-    return br
+    br.beforeGraph()
+    br
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -18,6 +18,6 @@ object CombineGVCFs {
     val cg = new CombineGVCFs(root)
     cg.variant = input
     cg.o = output
-    return cg
+    cg
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -18,6 +18,6 @@ object CombineVariants {
     val cv = new CombineVariants(root)
     cv.variant = input
     cv.out = output
-    return cv
+    cv
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -26,10 +26,10 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
   override val versionExitcode = List(0, 1)
   override def versionCommand = executable + " -jar " + jarFile + " -version"
 
-  override def getVersion = super.getVersion.collect { case version => "Gatk " + version }
+  override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
 
-  override def beforeGraph: Unit = {
-    super.beforeGraph
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
     if (reference_sequence == null) reference_sequence = referenceFasta()
   }
 }

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -29,6 +29,6 @@ object GenotypeGVCFs {
     val gg = new GenotypeGVCFs(root)
     gg.variant = gvcfFiles
     gg.out = output
-    return gg
+    gg
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -35,8 +35,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
     stand_emit_conf = config("stand_emit_conf", default = 0)
   }
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
     if (bamOutput != null && nct.getOrElse(1) > 1) {
       threads = 1
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -19,6 +19,6 @@ object IndelRealigner {
     ir.input_file :+= input
     ir.targetIntervals = targetIntervals
     ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
-    return ir
+    ir
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -18,6 +18,6 @@ object PrintReads {
     val br = new PrintReads(root)
     br.input_file :+= input
     br.out = output
-    return br
+    br
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -20,6 +20,6 @@ object RealignerTargetCreator {
     val re = new RealignerTargetCreator(root)
     re.input_file :+= input
     re.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.intervals")
-    return re
+    re
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -18,6 +18,6 @@ object SelectVariants {
     val sv = new SelectVariants(root)
     sv.variant = input
     sv.out = output
-    return sv
+    sv
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -26,8 +26,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
     }
   }
 
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
 
     genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
     nct = Some(getThreads(1))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -20,6 +20,6 @@ object VariantAnnotator {
     va.variant = input
     va.input_file = bamFiles
     va.out = output
-    return va
+    va
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -10,8 +10,8 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
-  override def beforeGraph {
-    super.beforeGraph
+  override def beforeGraph() {
+    super.beforeGraph()
   }
 }
 
@@ -22,8 +22,8 @@ object VariantEval {
     vareval.eval = Seq(sample)
     vareval.comp = Seq(compareWith)
     vareval.out = output
-    vareval.beforeGraph
-    return vareval
+    vareval.beforeGraph()
+    vareval
   }
 
   def apply(root: Configurable, sample: File, compareWith: File,
@@ -36,8 +36,8 @@ object VariantEval {
     vareval.ST = ST
     vareval.noEV = true
     vareval.EV = EV
-    vareval.beforeGraph
-    return vareval
+    vareval.beforeGraph()
+    vareval
   }
 
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -39,6 +39,6 @@ object VariantRecalibrator {
     vr.input :+= input
     vr.recal_file = recal_file
     vr.tranches_file = tranches_file
-    return vr
+    vr
   }
 }
\ No newline at end of file

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala

@@ -11,6 +11,8 @@ import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
 import org.broadinstitute.gatk.queue.QScript
 
 /**
+ * Basty pipeline including GATK steps
+ *
  * Created by pjvan_thof on 3/4/15.
  */
 class Basty(val root: Configurable) extends QScript with BastyTrait {

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

@@ -38,7 +38,7 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
     var gvcfPool: List[File] = Nil
     addGenotypingPipeline(gvcfPool)
 
-    while (todoGvcfs.size > 0) {
+    while (todoGvcfs.nonEmpty) {
       val index = Random.nextInt(todoGvcfs.size)
       gvcfPool ::= todoGvcfs(index)
       addGenotypingPipeline(gvcfPool)
@@ -51,8 +51,8 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
     gatkGenotyping.inputGvcfs = sampleGvcf :: gvcfPool
     gatkGenotyping.samples :+= sampleName
     gatkGenotyping.outputDir = new File(outputDir, "samples_" + gvcfPool.size)
-    gatkGenotyping.init
-    gatkGenotyping.biopetScript
+    gatkGenotyping.init()
+    gatkGenotyping.biopetScript()
     addAll(gatkGenotyping.functions)
   }
 }

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -38,7 +38,7 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
 
   def biopetScript() {
     addGenotypeGVCFs(inputGvcfs, outputFile)
-    if (!samples.isEmpty) {
+    if (samples.nonEmpty) {
       if (samples.size > 1) addSelectVariants(outputFile, samples, new File(outputDir, "samples/"), "all")
       for (sample <- samples) addSelectVariants(outputFile, List(sample), new File(outputDir, "samples/"), sample)
     }
@@ -47,7 +47,7 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
   def addGenotypeGVCFs(gvcfFiles: List[File], outputFile: File): File = {
     val genotypeGVCFs = GenotypeGVCFs(this, gvcfFiles, outputFile)
     add(genotypeGVCFs)
-    return genotypeGVCFs.out
+    genotypeGVCFs.out
   }
 
   def addSelectVariants(inputFile: File, samples: List[String], outputDir: File, name: String) {

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -78,8 +78,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
         val bamFile: Option[File] = if (config.contains("R1")) {
           mapping.input_R1 = config("R1")
           mapping.input_R2 = config("R2")
-          mapping.init
-          mapping.biopetScript
+          mapping.init()
+          mapping.biopetScript()
           addAll(mapping.functions) // Add functions of mapping to curent function pool
           Some(mapping.finalBamFile)
         } else if (config.contains("bam")) {
@@ -93,8 +93,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
             qscript.add(samToFastq)
             mapping.input_R1 = samToFastq.fastqR1
             mapping.input_R2 = Some(samToFastq.fastqR2)
-            mapping.init
-            mapping.biopetScript
+            mapping.init()
+            mapping.biopetScript()
             addAll(mapping.functions) // Add functions of mapping to curent function pool
             Some(mapping.finalBamFile)
           } else {
@@ -106,7 +106,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
               if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
               if (readGroup.getSample != sampleId || readGroup.getLibrary != libId) readGroupOke = false
             }
-            inputSam.close
+            inputSam.close()
 
             if (!readGroupOke) {
               if (config("correct_readgroups", default = false)) {
@@ -133,8 +133,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
         if (bamFile.isDefined) {
           gatkVariantcalling.inputBams = List(bamFile.get)
           gatkVariantcalling.variantcalling = config("library_variantcalling", default = false)
-          gatkVariantcalling.init
-          gatkVariantcalling.biopetScript
+          gatkVariantcalling.init()
+          gatkVariantcalling.biopetScript()
           addAll(gatkVariantcalling.functions)
         }
 
@@ -155,8 +155,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
         gatkVariantcalling.useHaplotypecaller = false
         gatkVariantcalling.useUnifiedGenotyper = false
       }
-      gatkVariantcalling.init
-      gatkVariantcalling.biopetScript
+      gatkVariantcalling.init()
+      gatkVariantcalling.biopetScript()
       addAll(gatkVariantcalling.functions)
 
       gatkVariantcalling.inputBams.foreach(x => addAll(Bam2Wig(qscript, x).functions))
@@ -174,7 +174,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   def biopetScript(): Unit = {
     addSamplesJobs()
 
-    addSummaryJobs
+    addSummaryJobs()
   }
 
   def addMultiSampleJobs(): Unit = {
@@ -184,13 +184,13 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       List(newFile)
     } else externalGvcfs ++ samples.map(_._2.gatkVariantcalling.scriptOutput.gvcfFile)
 
-    if (!skipGenotyping && gvcfFiles.size > 0) {
+    if (!skipGenotyping && gvcfFiles.nonEmpty) {
       if (jointGenotyping) {
         val gatkGenotyping = new GatkGenotyping(this)
         gatkGenotyping.inputGvcfs = gvcfFiles
         gatkGenotyping.outputDir = new File(outputDir, "genotyping")
-        gatkGenotyping.init
-        gatkGenotyping.biopetScript
+        gatkGenotyping.init()
+        gatkGenotyping.biopetScript()
         addAll(gatkGenotyping.functions)
         var vcfFile = gatkGenotyping.outputFile
       }
@@ -216,8 +216,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       multisampleVariantcalling.inputBams = allBamfiles.toList
       multisampleVariantcalling.outputDir = new File(outputDir, "variantcalling")
       multisampleVariantcalling.outputName = "multisample"
-      multisampleVariantcalling.init
-      multisampleVariantcalling.biopetScript
+      multisampleVariantcalling.init()
+      multisampleVariantcalling.biopetScript()
       addAll(multisampleVariantcalling.functions)
 
       if (config("inputtype", default = "dna").asString != "rna" && config("recalibration", default = false).asBoolean) {
@@ -225,8 +225,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
         recalibration.inputVcf = multisampleVariantcalling.scriptOutput.finalVcfFile
         recalibration.bamFiles = allBamfiles
         recalibration.outputDir = new File(outputDir, "recalibration")
-        recalibration.init
-        recalibration.biopetScript
+        recalibration.init()
+        recalibration.biopetScript()
       }
     }
   }