Fix code style warnings by IDE

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

@@ -72,8 +72,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
     /** Sample specific files to add to summary */
     def summaryFiles: Map[String, File] = {
       preProcessBam match {
-        case Some(preProcessBam) => Map("preProcessBam" -> preProcessBam)
-        case _                   => Map()
+        case Some(b) => Map("preProcessBam" -> b)
+        case _       => Map()
       }
     }
 
@@ -88,9 +88,9 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
       /** Library specific files to add to the summary */
       def summaryFiles: Map[String, File] = {
         (bamFile, preProcessBam) match {
-          case (Some(bamFile), Some(preProcessBam)) => Map("bamFile" -> bamFile, "preProcessBam" -> preProcessBam)
-          case (Some(bamFile), _)                   => Map("bamFile" -> bamFile)
-          case _                                    => Map()
+          case (Some(b), Some(pb)) => Map("bamFile" -> b, "preProcessBam" -> pb)
+          case (Some(b), _)        => Map("bamFile" -> b)
+          case _                   => Map()
         }
       }
 
@@ -116,10 +116,9 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
           case (false, true) => // Starting from bam file
             config("bam_to_fastq", default = false).asBoolean match {
               case true => makeMapping // bam file will be converted to fastq
-              case false => {
+              case false =>
                 val file = new File(libDir, sampleId + "-" + libId + ".final.bam")
                 (None, Some(file), preProcess(file))
-              }
             }
           case _ => (None, None, None)
         }
@@ -137,7 +136,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
             mapping.input_R2 = config("R2")
           })
           case (false, true) => config("bam_to_fastq", default = false).asBoolean match {
-            case true => {
+            case true =>
               val samToFastq = SamToFastq(qscript, config("bam"),
                 new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
                 new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
@@ -147,8 +146,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
                 mapping.input_R1 = samToFastq.fastqR1
                 mapping.input_R2 = Some(samToFastq.fastqR2)
               })
-            }
-            case false => {
+            case false =>
               val inputSam = SamReaderFactory.makeDefault.open(config("bam"))
               val readGroups = inputSam.getFileHeader.getReadGroups
 
@@ -157,7 +155,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
                 if (readGroup.getLibrary != libId) logger.warn("Library ID readgroup in bam file is not the same")
                 readGroup.getSample == sampleId && readGroup.getLibrary == libId
               })
-              inputSam.close
+              inputSam.close()
 
               if (!readGroupOke) {
                 if (config("correct_readgroups", default = false).asBoolean) {
@@ -181,15 +179,13 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
                 bamLn.deps :+= baiLn.output
                 add(bamLn)
               }
-
-            }
           }
           case _ => logger.warn("Sample: " + sampleId + "  Library: " + libId + ", no reads found")
         }
 
         mapping.foreach(mapping => {
-          mapping.init
-          mapping.biopetScript
+          mapping.init()
+          mapping.biopetScript()
           addAll(mapping.functions) // Add functions of mapping to curent function pool
           addSummaryQScript(mapping)
         })
@@ -234,13 +230,13 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
       }
     }
 
-    lazy val preProcessBam: Option[File] = addDoublePreProcess(libraries.map(lib => {
+    lazy val preProcessBam: Option[File] = addDoublePreProcess(libraries.flatMap(lib => {
       (lib._2.bamFile, lib._2.preProcessBam) match {
         case (_, Some(file)) => Some(file)
         case (Some(file), _) => Some(file)
         case _               => None
       }
-    }).flatten.toList)
+    }).toList)
 
     lazy val variantcalling = if (config("single_sample_variantcalling", default = false).asBoolean) {
       Some(makeVariantcalling(multisample = true))
@@ -255,8 +251,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
         bamMetrics.sampleId = Some(sampleId)
         bamMetrics.inputBam = preProcessBam.get
         bamMetrics.outputDir = sampleDir
-        bamMetrics.init
-        bamMetrics.biopetScript
+        bamMetrics.init()
+        bamMetrics.biopetScript()
         addAll(bamMetrics.functions)
         addSummaryQScript(bamMetrics)
 
@@ -281,7 +277,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
   def addMultiSampleJobs(): Unit = {
     variantcalling.foreach(vc => {
       vc.outputDir = new File(outputDir, "variantcalling")
-      vc.inputBams = samples.map(_._2.preProcessBam).flatten.toList
+      vc.inputBams = samples.flatMap(_._2.preProcessBam).toList
       vc.init
       vc.biopetScript
       addAll(vc.functions)