Fix style

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
-import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
 import nl.lumc.sasc.biopet.utils._
-import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
 
 import scala.collection.JavaConversions._
 
@@ -185,7 +185,8 @@ object Reference {
         s"""Species found in general config:
            |- ${globalSpecies.keys.toList.sorted.mkString("\n- ")}
            |$warn
-           |""".stripMargin else s"No references found in global config. $warn"))
+           |""".stripMargin
+      else s"No references found in global config. $warn"))
 
     val globalReferences = globalSpecies.getOrElse(species, Map()).asInstanceOf[Map[String, Any]]
     val referenceName = Question.string("reference_name",
@@ -193,7 +194,8 @@ object Reference {
         s"""Reference for $species found in general config:
             |- ${globalReferences.keys.toList.sorted.mkString("\n- ")}
             |$warn
-            |""".stripMargin else s"No references found in global config. $warn"))
+            |""".stripMargin
+      else s"No references found in global config. $warn"))
 
     val reference = globalReferences.getOrElse(referenceName, Map()).asInstanceOf[Map[String, Any]]
     val referenceFasta: Option[String] = if (reference.contains("reference_fasta")) None else {

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

@@ -4,11 +4,11 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.utils.summary.Summary
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Question, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Question, ToolCommand }
 
 /**
-  * Created by pjvanthof on 17/12/2016.
-  */
+ * Created by pjvanthof on 17/12/2016.
+ */
 trait TemplateTool extends ToolCommand {
   import TemplateTool._
   case class Args(expert: Boolean = false) extends AbstractArgs
@@ -20,10 +20,10 @@ trait TemplateTool extends ToolCommand {
   }
 
   /**
-    * Program will split fastq file in multiple fastq files
-    *
-    * @param args the command line arguments
-    */
+   * Program will split fastq file in multiple fastq files
+   *
+   * @param args the command line arguments
+   */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
     val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
@@ -84,7 +84,7 @@ object TemplateTool {
           val sizes = configs.map(new Summary(_)).map(x => (x.samples.size, x.libraries.map(_._2.size).sum))
           val samples = sizes.map(_._1).sum
           val libs = sizes.map(_._2).sum
-          val mergedConfig = new Summary(configs.foldLeft(Map[String, Any]())((a,b) => ConfigUtils.mergeMaps(a, b)))
+          val mergedConfig = new Summary(configs.foldLeft(Map[String, Any]())((a, b) => ConfigUtils.mergeMaps(a, b)))
           val mergesSamples = mergedConfig.samples.size
           val mergesLibraries = mergedConfig.libraries.map(_._2.size).sum
           if (mergesSamples != samples) println("WARNING: Overlapping samples detected")

biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

@@ -15,7 +15,7 @@
 package nl.lumc.sasc.biopet
 
 import nl.lumc.sasc.biopet.core.PipelineStatus
-import nl.lumc.sasc.biopet.utils.{BiopetExecutable, MainCommand}
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
 
 object BiopetExecutableMain extends BiopetExecutable {
   def pipelines: List[MainCommand] = List(

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala

 package nl.lumc.sasc.biopet.utils
 
 /**
-  * Created by pjvanthof on 16/12/2016.
-  */
+ * Created by pjvanthof on 16/12/2016.
+ */
 object Question {
 
   def string(name: String,
@@ -31,8 +31,8 @@ object Question {
   }
 
   def boolean(name: String,
-             default: Option[Boolean] = None,
-             description: Option[String] = None): Boolean = {
+              default: Option[Boolean] = None,
+              description: Option[String] = None): Boolean = {
     description.foreach(println)
     default.foreach(x => println(s"Default value: $x"))
     print(s"$name (y/n) > ")

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/template/MultiSampleMapping.scala

@@ -2,12 +2,12 @@ package nl.lumc.sasc.biopet.pipelines.mapping.template
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, TemplateTool}
+import nl.lumc.sasc.biopet.core.{ Reference, TemplateTool }
 import nl.lumc.sasc.biopet.utils.Question
 
 /**
-  * Created by pjvanthof on 17/12/2016.
-  */
+ * Created by pjvanthof on 17/12/2016.
+ */
 object MultiSampleMapping extends TemplateTool {
 
   override lazy val sampleConfigs: List[File] = TemplateTool.askSampleConfigs()
@@ -19,10 +19,10 @@ object MultiSampleMapping extends TemplateTool {
     val referenceConfig = map ++ Reference.askReference
 
     val aligner = if (map.contains("aligner")) map("aligner").toString
-    else  Question.string("Aligner", posibleValues = possibleAligners, default = Some("bwa-mem"))
+    else Question.string("Aligner", posibleValues = possibleAligners, default = Some("bwa-mem"))
 
     referenceConfig ++ Map(
       "aligner" -> aligner
-      )
+    )
   }
 }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

@@ -178,14 +178,14 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
 object ShivaVariantcalling extends PipelineCommand {
   /** Will generate all available variantcallers */
   protected[shiva] def callersList(root: Configurable): List[Variantcaller] =
-  new HaplotypeCallerGvcf(root) ::
-    new HaplotypeCallerAllele(root) ::
-    new UnifiedGenotyperAllele(root) ::
-    new UnifiedGenotyper(root) ::
-    new HaplotypeCaller(root) ::
-    new Freebayes(root) ::
-    new RawVcf(root) ::
-    new Bcftools(root) ::
-    new BcftoolsSingleSample(root) ::
-    new VarscanCnsSingleSample(root) :: Nil
+    new HaplotypeCallerGvcf(root) ::
+      new HaplotypeCallerAllele(root) ::
+      new UnifiedGenotyperAllele(root) ::
+      new UnifiedGenotyper(root) ::
+      new HaplotypeCaller(root) ::
+      new Freebayes(root) ::
+      new RawVcf(root) ::
+      new Bcftools(root) ::
+      new BcftoolsSingleSample(root) ::
+      new VarscanCnsSingleSample(root) :: Nil
 }
\ No newline at end of file

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala

@@ -8,8 +8,8 @@ import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
 import nl.lumc.sasc.biopet.utils.Question
 
 /**
-  * Created by pjvanthof on 17/12/2016.
-  */
+ * Created by pjvanthof on 17/12/2016.
+ */
 object Shiva extends TemplateTool {
 
   override lazy val sampleConfigs: List[File] = TemplateTool.askSampleConfigs()
@@ -30,6 +30,6 @@ object Shiva extends TemplateTool {
       "variantcallers" -> variantCallers,
       "use_indel_realigner" -> useIndelRealigner,
       "use_base_recalibration" -> useBaseRecalibration
-      )
+    )
   }
 }