Style issues

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

@@ -30,7 +30,8 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
     * Gets location of compiled class of pipeline
     * @return path from classPath to class file
     */
-  def pipeline: String = "/" + getClass.getName.takeWhile(_ != '$').replaceAll("\\.", "/") + ".class"
+  def pipeline: String =
+    "/" + getClass.getName.takeWhile(_ != '$').replaceAll("\\.", "/") + ".class"
 
   def pipelineName: String = getClass.getName.takeWhile(_ != '$').split("\\.").last.toLowerCase
 

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -64,27 +64,27 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
       qscript match {
         case s: MultiSampleQScript => s.initSummaryDb()
         case t: SampleLibraryTag =>
-          t.sampleId.foreach {
-            sampleName =>
-              val sampleId = Await
-                .result(db.getSamples(name = Some(sampleName), runId = Some(qscript.summaryRunId))
-                  .map(_.headOption.map(_.id)),
-                  Duration.Inf)
-                .getOrElse {
-                  Await.result(db.createOrUpdateSample(sampleName, qscript.summaryRunId),
-                    Duration.Inf)
-                }
-              t.libId.foreach { libName =>
-                Await.result(db.getSamples(name = Some(libName),
-                  runId = Some(qscript.summaryRunId),
-                  sampleId = Some(sampleId))
-                  .map(_.headOption.map(_.id)),
-                  Duration.Inf)
-                  .getOrElse {
-                    Await.result(db.createOrUpdateLibrary(libName, qscript.summaryRunId, sampleId),
+          t.sampleId.foreach { sampleName =>
+            val sampleId = Await
+              .result(db.getSamples(name = Some(sampleName), runId = Some(qscript.summaryRunId))
+                        .map(_.headOption.map(_.id)),
                       Duration.Inf)
-                  }
+              .getOrElse {
+                Await.result(db.createOrUpdateSample(sampleName, qscript.summaryRunId),
+                             Duration.Inf)
               }
+            t.libId.foreach { libName =>
+              Await
+                .result(db.getSamples(name = Some(libName),
+                                      runId = Some(qscript.summaryRunId),
+                                      sampleId = Some(sampleId))
+                          .map(_.headOption.map(_.id)),
+                        Duration.Inf)
+                .getOrElse {
+                  Await.result(db.createOrUpdateLibrary(libName, qscript.summaryRunId, sampleId),
+                               Duration.Inf)
+                }
+            }
           }
         case _ => qscript.summaryRunId
       }

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala

@@ -210,7 +210,8 @@ object MultiSampleQScriptTest {
     )
   )
 
-  def apply(configs: List[Map[String, Any]], only: List[String] = Nil): QScript with MultiSampleQScript {
+  def apply(configs: List[Map[String, Any]],
+            only: List[String] = Nil): QScript with MultiSampleQScript {
     def init(): Unit
 
     def getLastLogMessage: String

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PedigreeQScriptTest.scala

@@ -171,7 +171,8 @@ object PedigreeQScriptTest {
 
   val trioPed = Map("ped_file" -> resourcePath("/trio.ped"))
 
-  def apply(configs: List[Map[String, Any]], only: List[String] = Nil): QScript with PedigreeQscript {
+  def apply(configs: List[Map[String, Any]],
+            only: List[String] = Nil): QScript with PedigreeQscript {
     def init(): Unit
 
     def biopetScript(): Unit

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala

@@ -33,8 +33,10 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
   case class Qfunc(in: Seq[File], out: Seq[File]) extends QFunction {
     override def inputs: Seq[File] = in
     override def outputs: Seq[File] = out
-    override def doneOutputs: Seq[File] = out.map(x => new File(x.getParentFile, s".${x.getName}.done"))
-    override def failOutputs: Seq[File] = out.map(x => new File(x.getParentFile, s".${x.getName}.fail"))
+    override def doneOutputs: Seq[File] =
+      out.map(x => new File(x.getParentFile, s".${x.getName}.done"))
+    override def failOutputs: Seq[File] =
+      out.map(x => new File(x.getParentFile, s".${x.getName}.fail"))
     jobOutputFile = new File(out.head + ".out")
   }
 

biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala

@@ -65,7 +65,8 @@ class VcfFilterTest extends TestNGSuite with Matchers {
   @Test def testMinQualScore(): Unit = testCommand(minQualScore = Some(50.0))
   @Test def testFilterHetVarToHomVar(): Unit = testCommand(filterHetVarToHomVar = List("dummy"))
   @Test def testId(): Unit = testCommand(id = List("rs01", "rs02"))
-  @Test def testIdFile(): Unit = testCommand(idFile = Some(File.createTempFile("vcfFilter", ".txt")))
+  @Test def testIdFile(): Unit =
+    testCommand(idFile = Some(File.createTempFile("vcfFilter", ".txt")))
 
   protected def testCommand(minSampleDepth: Option[Int] = None,
                             minTotalDepth: Option[Int] = None,