Biopet core code inspection round

Jenkinsfile

@@ -29,7 +29,7 @@ node('local') {
             sh 'mkdocs build --clean --strict'
         }
 
-        if (currentBuild.result == null || "SUCCESS".equals(currentBuild.result)) {
+        if (currentBuild.result == null || "SUCCESS" == currentBuild.result) {
             currentBuild.result = "SUCCESS"
             slackSend(color: '#00FF00', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')
         } else {
@@ -37,7 +37,7 @@ node('local') {
         }
 
     } catch (e) {
-        if (currentBuild.result == null || "FAILED".equals(currentBuild.result)) {
+        if (currentBuild.result == null || "FAILED" == currentBuild.result) {
             currentBuild.result = "FAILED"
         }
         slackSend(color: '#FF0000', message: "${currentBuild.result}: Job '${env.JOB_NAME} #${env.BUILD_NUMBER}' (<${env.BUILD_URL}|Open>)", channel: '#biopet-bot', teamDomain: 'lumc', tokenCredentialId: 'lumc')

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css

@@ -150,10 +150,9 @@ body {
      float:right;
      width:0;
      height:0;
-     border-color:transparent;
-     border-style:solid;
-     border-width:5px 0 5px 5px;
-     border-left-color:#cccccc;
+     border: 5px solid transparent;
+     border-right-width: 0;
+     border-left-color: #cccccc;
      margin-top:5px;
      margin-right:-10px;
  }

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css

@@ -46,9 +46,7 @@ table[data-sortable] th:after {
     vertical-align: inherit;
     height: 0;
     width: 0;
-    border-width: 5px;
-    border-style: solid;
-    border-color: transparent;
+    border: 5px solid transparent;
     margin-right: 1px;
     margin-left: 10px;
     float: right;

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/files.ssp

@@ -31,9 +31,9 @@
 <tbody>
 #for (file <- files)
     <tr><td>${allPipelines.find(_.id == file.pipelineId).map(_.name)}</td>
-    <td>${file.moduleId.map(id => allModules.find(x => x.pipelineId == file.pipelineId && file.moduleId == id).map(_.name)).flatten.getOrElse(("-"))}</td>
-    <td>${file.sampleId.map(id => allSamples.find(_.id == id).map(_.name)).flatten.getOrElse(("-"))}</td>
-    <td>${file.libraryId.map(id => allLibraries.find(_.id == id).map(_.name)).flatten.getOrElse(("-"))}</td>
+    <td>${file.moduleId.flatMap(id => allModules.find(x => x.pipelineId == file.pipelineId && file.moduleId == id).map(_.name)).getOrElse("-")}</td>
+    <td>${file.sampleId.flatMap(id => allSamples.find(_.id == id).map(_.name)).getOrElse("-")}</td>
+    <td>${file.libraryId.flatMap(id => allLibraries.find(_.id == id).map(_.name)).getOrElse("-")}</td>
     <td>${file.key}</td>
     <td>${file.path}</td>
     <td>${file.md5}</td></tr>

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp

@@ -42,7 +42,7 @@
             val tabIndex = if (first) " tabindex='-1'" else ""
 //            val listGroupA = if(subPage._2.subPages.nonEmpty) "list-group-item" else ""
 
-            var menuItem: String = "<li class='%s'>".format(listSubmenu) +
+            val menuItem: String = "<li class='%s'>".format(listSubmenu) +
             "<a href='%s' class='%s'%s>".format(href, "", tabIndex) +
             "%s".format(subPageName) +
             "</a>" +
@@ -93,7 +93,7 @@
         <script language="JavaScript">
             <!--
             $(document).ready(function() {
-                Sortable.init()
+                Sortable.init();
 
                 $('body').scrollspy({
                     target: '.bs-sidebar'
@@ -135,14 +135,14 @@
                         <a href="${rootPath}index.html">Home
                             #if (iPage.subPages.nonEmpty) <b class="caret"></b> #end
                         </a>
-                        ${unescape(createMenu(iPage, Nil, false))}
+                        ${unescape(createMenu(iPage, Nil, first = false))}
                     </li>
                 #else
                     <li class="root #if (t == path.size) active #end">
                         <a href="${rootPath}${path.slice(0,t).mkString("", "/", "/")}index.html">${path( t - 1 )}
                             #if (getSubPage(path.slice(0, t)).subPages.nonEmpty) <b class="caret"></b> #end
                         </a>
-                        ${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t), false))}
+                        ${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t), first = false))}
                     </li>
                 #end
             #end

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

@@ -60,10 +60,10 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   }
 
   /**
-    *  This value is used to let you job wait a x number of second after it finish.
-    *  This is ionly used when having storage delay issues
+    * This value is used to let you job wait a x number of second after it finish.
+    * This is ionly used when having storage delay issues
     */
-  var jobDelayTime: Option[Int] = config("job_delay_time")
+  val jobDelayTime: Option[Int] = config("job_delay_time")
 
   // This overrides the default "sh" from queue. For Biopet the default is "bash"
   updateJobRun = {
@@ -147,9 +147,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   }
 
   private[core] var _inputAsStdin = false
-  def inputAsStdin = _inputAsStdin
+  def inputAsStdin: Boolean = _inputAsStdin
   private[core] var _outputAsStdout = false
-  def outputAsStdout = _outputAsStdout
+  def outputAsStdout: Boolean = _outputAsStdout
 
   /**
     * This operator sends stdout to `that` and combine this into 1 command line function
@@ -212,13 +212,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
                maxGroups: Int = 0): String = {
     if (values.size % groupSize != 0)
       Logging.addError(
-        s"Arg '${argName}' values: '${values}' does not fit to a groupSize of ${groupSize}")
+        s"Arg '$argName' values: '$values' does not fit to a groupSize of $groupSize")
     val groups = values.size / groupSize
     if (groups < minGroups)
-      Logging.addError(s"Args '${argName}' need atleast $minGroups with size $groupSize")
+      Logging.addError(s"Args '$argName' need atleast $minGroups with size $groupSize")
     if (maxGroups > 0 && groups > maxGroups)
-      Logging.addError(s"Args '${argName}' may only have $maxGroups with size $groupSize")
-    if (values.nonEmpty) required(argName) + values.map(required(_)).mkString
+      Logging.addError(s"Args '$argName' may only have $maxGroups with size $groupSize")
+    if (values.nonEmpty) required(argName) + values.map(required).mkString
     else ""
   }
 
@@ -251,7 +251,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
   }
 
   private[core] var _pipesJobs: List[BiopetCommandLineFunction] = Nil
-  def pipesJobs = _pipesJobs
+  def pipesJobs: List[BiopetCommandLineFunction] = _pipesJobs
   def addPipeJob(job: BiopetCommandLineFunction) {
     _pipesJobs :+= job
     _pipesJobs = _pipesJobs.distinct

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

@@ -30,7 +30,7 @@ trait BiopetJavaCommandLineFunction
   override def defaultVmemFactor: Double = 2.0
 
   /** Constructs java opts, this adds scala threads */
-  override def javaOpts =
+  override def javaOpts: String =
     super.javaOpts +
       optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false) +
       optional("-Dscala.concurrent.context.maxThreads=", threads, spaceSeparated = false)

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

@@ -30,14 +30,14 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
   lazy val input: List[File] = try {
     commands.flatMap(_.inputs)
   } catch {
-    case e: Exception => Nil
+    case _: Exception => Nil
   }
 
   @Output
   lazy val output: List[File] = try {
     commands.flatMap(_.outputs)
   } catch {
-    case e: Exception => Nil
+    case _: Exception => Nil
   }
 
   _pipesJobs :::= commands
@@ -74,7 +74,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
   override def defaultThreads = 0
 
   val parent: Configurable = commands.head.parent
-  override def configNamespace = commands.map(_.configNamespace).mkString("-")
+  override def configNamespace: String = commands.map(_.configNamespace).mkString("-")
   def cmdLine: String = {
     "(" + commands.head.cmdLine + (if (commands.head.stdinFile.isDefined) {
                                      " < " + required(

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

@@ -221,7 +221,7 @@ object BiopetQScript {
     try {
       Some(function.inputs)
     } catch {
-      case e: NullPointerException => None
+      case _: NullPointerException => None
     }
   }
 
@@ -229,7 +229,7 @@ object BiopetQScript {
     try {
       Some(function.outputs)
     } catch {
-      case e: NullPointerException => None
+      case _: NullPointerException => None
     }
   }
 
@@ -237,7 +237,7 @@ object BiopetQScript {
     try {
       Some(function.doneOutputs)
     } catch {
-      case e: NullPointerException => None
+      case _: NullPointerException => None
     }
   }
 
@@ -245,7 +245,7 @@ object BiopetQScript {
     try {
       Some(function.failOutputs)
     } catch {
-      case e: NullPointerException => None
+      case _: NullPointerException => None
     }
   }
 
@@ -253,7 +253,7 @@ object BiopetQScript {
     try {
       Some(function.isDone)
     } catch {
-      case e: NullPointerException => None
+      case _: NullPointerException => None
     }
   }
 
@@ -261,7 +261,7 @@ object BiopetQScript {
     try {
       Some(function.isFail)
     } catch {
-      case e: NullPointerException => None
+      case _: NullPointerException => None
     }
   }
 

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

@@ -32,7 +32,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
   def defaultThreads = 1
 
   /** This method will get and set the cores requested */
-  final def threads = nCoresRequest match {
+  final def threads: Int = nCoresRequest match {
     case Some(i) => i
     case _ =>
       val t = getThreads
@@ -47,14 +47,15 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
   def defaultCoreMemory: Double = 2.0
   def defaultVmemFactor: Double = 1.4
   def defaultResidentFactor: Double = 1.2
-  var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
+
+  val vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
 
   val useSge: Boolean = config("use_sge", default = true)
 
-  var residentFactor: Double = config("resident_factor", default = defaultResidentFactor)
+  val residentFactor: Double = config("resident_factor", default = defaultResidentFactor)
 
   private var _coreMemory: Double = 2.0
-  def coreMemory = _coreMemory
+  def coreMemory: Double = _coreMemory
 
   /** This value is for SGE and is defined in seconds */
   wallTime = config("max_walltime")
@@ -92,7 +93,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
     val firstOutput = try {
       this.firstOutput
     } catch {
-      case e: NullPointerException => null
+      case _: NullPointerException => null
     }
 
     nCoresRequest = Option(threads)

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

@@ -25,6 +25,7 @@ import org.broadinstitute.gatk.queue.QScript
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration
 import scala.concurrent.ExecutionContext.Implicits.global
+import scala.util.matching.Regex
 
 /** This trait creates a structured way of use multisample pipelines */
 trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
@@ -84,7 +85,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
                namespace = libId,
                path = List("samples", sampleId, "libraries"))
 
-      def sampleId = sample.sampleId
+      def sampleId: String = sample.sampleId
 
       lazy val libGroups: List[String] = libTags.get("groups") match {
         case Some(g: List[_]) => g.map(_.toString)
@@ -109,19 +110,19 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
              namespace = sampleId,
              path = List("samples"))
 
-    lazy val gender = {
+    lazy val gender: MultiSampleQScript.Gender.Value = {
       val g: Option[String] = sampleTags.get("gender").map(_.toString)
       g.map(_.toLowerCase) match {
         case Some("male") => Gender.Male
         case Some("female") => Gender.Female
-        case Some(s) =>
+        case Some(_) =>
           logger.warn(s"Could not convert '$g' to a gender")
           Gender.Unknown
         case _ => Gender.Unknown
       }
     }
 
-    lazy val father = {
+    lazy val father: Option[String] = {
       val g: Option[String] = sampleTags.get("father").map(_.toString)
       g.foreach { father =>
         if (sampleId == father) Logging.addError(s"Father for $sampleId can not be itself")
@@ -133,7 +134,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
       g
     }
 
-    lazy val mother = {
+    lazy val mother: Option[String] = {
       val g: Option[String] = sampleTags.get("mother").map(_.toString)
       g.foreach { mother =>
         if (sampleId == mother) Logging.addError(s"mother for $sampleId can not be itself")
@@ -199,7 +200,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
 
     /** function add all libraries in one call */
     protected final def addPerLibJobs(): Unit = {
-      for ((libId, library) <- libraries) {
+      for ((_, library) <- libraries) {
         library.addAndTrackJobs()
       }
     }
@@ -228,8 +229,8 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
   protected def sampleIds: Set[String] =
     ConfigUtils.any2map(globalConfig.map.getOrElse("samples", Map())).keySet
 
-  protected lazy val nameRegex = """^[a-zA-Z0-9][a-zA-Z0-9-_]+[a-zA-Z0-9]$""".r
-  protected lazy val nameError = "has an invalid name. " +
+  protected lazy val nameRegex: Regex = """^[a-zA-Z0-9][a-zA-Z0-9-_]+[a-zA-Z0-9]$""".r
+  protected lazy val nameError: String = "has an invalid name. " +
     "Sample names must have at least 3 characters, " +
     "must begin and end with an alphanumeric character, " +
     "and must not have whitespace and special characters. " +
@@ -281,7 +282,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     sample ::: lib ::: super.configFullPath
   }
 
-  def initSummaryDb: Unit = {
+  def initSummaryDb(): Unit = {
     val db = SummaryDb.openSqliteSummary(summaryDbFile)
     val namesOld = Await.result(db.getSamples(runId = Some(summaryRunId)).map(_.map(_.name).toSet),
                                 Duration.Inf)

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

@@ -201,10 +201,7 @@ trait PedigreeQscript extends MultiSampleQScript { qscript: QScript =>
       }
       val affectedField = p.affectedPhenotype match {
         case Some(b) =>
-          b match {
-            case true => "2"
-            case _ => "1"
-          }
+          if (b) "2" else "1"
         case _ => "0"
       }
       val mainLine: String =

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

@@ -30,11 +30,11 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
     * Gets location of compiled class of pipeline
     * @return path from classPath to class file
     */
-  def pipeline = "/" + getClass.getName.takeWhile(_ != '$').replaceAll("\\.", "/") + ".class"
+  def pipeline: String = "/" + getClass.getName.takeWhile(_ != '$').replaceAll("\\.", "/") + ".class"
 
-  def pipelineName = getClass.getName.takeWhile(_ != '$').split("\\.").last.toLowerCase
+  def pipelineName: String = getClass.getName.takeWhile(_ != '$').split("\\.").last.toLowerCase
 
-  protected val globalConfig = Config.global
+  protected val globalConfig: Config = Config.global
 
   /** Class can be used directly from java with -cp option */
   def main(args: Array[String]): Unit = {

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

@@ -16,6 +16,7 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 
+import htsjdk.samtools.SAMSequenceDictionary
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
 import nl.lumc.sasc.biopet.utils._
@@ -50,15 +51,15 @@ trait Reference extends Configurable {
     }
   }
 
-  def referenceDict = FastaUtils.getCachedDict(referenceFasta())
+  def referenceDict: SAMSequenceDictionary = FastaUtils.getCachedDict(referenceFasta())
 
   /** All config values will get a prefix */
-  override def subPath = {
+  override def subPath: List[String] = {
     referenceConfigPath ::: super.subPath
   }
 
   lazy val geneAnnotationVersion: Option[String] = config("gene_annotation_name")
-  lazy val geneAnnotationSubPath =
+  lazy val geneAnnotationSubPath: List[String] =
     geneAnnotationVersion.map(List("gene_annotations", _)).getOrElse(Nil)
   lazy val dbsnpVersion: Option[String] = config("dbsnp_version")
   lazy val dbsnpSubPath: List[String] =
@@ -66,7 +67,7 @@ trait Reference extends Configurable {
   def dbsnpVcfFile: Option[File] = config("dbsnp_vcf", extraSubPath = dbsnpSubPath)
 
   /** Returns the reference config path */
-  def referenceConfigPath = {
+  def referenceConfigPath: List[String] = {
     List("references", referenceSpecies, referenceName)
   }
 
@@ -74,7 +75,7 @@ trait Reference extends Configurable {
   def faiRequired = false
 
   /** When set override this on true the pipeline with raise an exception when dict index is not found */
-  def dictRequired = this.isInstanceOf[Summarizable] || this.isInstanceOf[SummaryQScript]
+  def dictRequired: Boolean = this.isInstanceOf[Summarizable] || this.isInstanceOf[SummaryQScript]
 
   /** Returns the dict file belonging to the fasta file */
   def referenceDictFile =

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

@@ -42,7 +42,7 @@ trait TemplateTool extends ToolCommand {
     opt[File]('t', "template") valueName "<file>" action { (x, c) =>
       c.copy(template = Some(x))
     } text "Path to template. By default it will try to fetch this from the ENV value 'BIOPET_SCRIPT_TEMPLATE'"
-    opt[Unit]("expert") action { (x, c) =>
+    opt[Unit]("expert") action { (_, c) =>
       c.copy(expert = true)
     } text "This enables expert options / questions"
   }
@@ -149,7 +149,6 @@ object TemplateTool {
         val files = configFile :: currentList
         if (files.size > 1) {
           val configs = files.map(f => new Summary(ConfigUtils.fileToConfigMap(f)))
-          val sizes = configs.map(x => (x.samples.size, x.libraries.map(_._2.size).sum))
           val samples = configs.flatMap(_.samples.toList)
           val libs = configs.flatMap(_.libraries.flatMap {
             case (s, libs) => libs.toList.map(l => (s, l))

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

@@ -16,6 +16,8 @@ package nl.lumc.sasc.biopet.core
 
 import nl.lumc.sasc.biopet.FullVersion
 
+import scala.util.matching.Regex
+
 /**
   * Created by pjvanthof on 11/09/15.
   */
@@ -23,7 +25,7 @@ trait ToolCommandFunction extends BiopetJavaCommandLineFunction with Version {
   def toolObject: Object
 
   def versionCommand = ""
-  def versionRegex = "".r
+  def versionRegex: Regex = "".r
 
   override def getVersion = Some("Biopet " + FullVersion)
 

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

@@ -66,8 +66,8 @@ object Version extends Logging {
   private[core] def getVersionInternal(versionCommand: String,
                                        versionRegex: Regex,
                                        versionExitcode: List[Int] = List(0)): Option[String] = {
-    if (versionCache.contains(versionCommand)) return versionCache.get(versionCommand)
-    else if (versionCommand == null || versionRegex == null) return None
+    if (versionCache.contains(versionCommand)) versionCache.get(versionCommand)
+    else if (versionCommand == null || versionRegex == null) None
     else {
       val stdout = new StringBuffer()
       val stderr = new StringBuffer()

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/CheckChecksum.scala

@@ -36,7 +36,7 @@ class CheckChecksum extends InProcessFunction {
   var checksum: String = _
 
   /** Exits whenever the input md5sum is not the same as the output md5sum */
-  def run: Unit = {
+  def run(): Unit = {
     val outputChecksum = WriteSummary.parseChecksum(checksumFile).toLowerCase
 
     if (outputChecksum != checksum.toLowerCase) {

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala

@@ -16,10 +16,12 @@ package nl.lumc.sasc.biopet.core.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
+import scala.util.matching.Regex
+
 /** Extension for md5sum */
 class Md5sum(val parent: Configurable) extends BiopetCommandLineFunction with Version {
   mainFunction = false
@@ -32,11 +34,11 @@ class Md5sum(val parent: Configurable) extends BiopetCommandLineFunction with Ve
 
   executable = config("exe", default = "md5sum")
 
-  def versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
-  def versionCommand = executable + " --version"
+  def versionRegex: Regex = """md5sum \(GNU coreutils\) (.*)""".r
+  def versionCommand: String = executable + " --version"
 
   /** return commandline to execute */
-  def cmdLine = required(executable) + required(input) + " > " + required(output)
+  def cmdLine: String = required(executable) + required(input) + " > " + required(output)
 }
 
 /** Object for constructors for md5sum */

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -74,7 +74,7 @@ trait ReportBuilderExtension extends ToolCommandFunction {
 
 trait ReportBuilder extends ToolCommand {
 
-  implicit lazy val ec = ReportBuilder.ec
+  implicit lazy val ec: ExecutionContextExecutor = ReportBuilder.ec
   implicit def toOption[T](x: T): Option[T] = Option(x)
   implicit def autoWait[T](x: Future[T]): T = Await.result(x, Duration.Inf)
 
@@ -242,9 +242,8 @@ trait ReportBuilder extends ToolCommand {
       try {
         Await.result(Future.sequence(futures), Duration.fromNanos(30000000000L))
       } catch {
-        case e: TimeoutException =>
+        case _: TimeoutException =>
       }
-      val dones = futures.filter(_.isCompleted)
       val notDone = futures.filter(!_.isCompleted)
       done += futures.size - notDone.size
       if (notDone.nonEmpty) {
@@ -364,8 +363,7 @@ trait ReportBuilder extends ToolCommand {
           dbFiles
             .map(
               x =>
-                x.get(pipelinelineId.get)
-                  .getOrElse(Seq())
+                x.getOrElse(pipelinelineId.get, Seq())
                   .filter(_.moduleId.isEmpty)))
 
     modulePages
@@ -398,7 +396,7 @@ trait ReportBuilder extends ToolCommand {
 
 object ReportBuilder {
 
-  implicit lazy val ec = ExecutionContext.global
+  implicit lazy val ec: ExecutionContextExecutor = ExecutionContext.global
 
   /** Single template render engine, this will have a cache for all compile templates */
   protected val engine = new TemplateEngine()

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

@@ -44,7 +44,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
   private[summary] var summaryQScripts: List[SummaryQScript] = Nil
 
   /** Name of the pipeline in the summary */
-  var summaryName = configNamespace
+  var summaryName: String = configNamespace
 
   /** Must return a map with used settings for this pipeline */
   def summarySettings: Map[String, Any]
@@ -98,7 +98,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
       Await.result(
         SummaryDb.openSqliteSummary(summaryDbFile).getRuns(runId = Some(id)).map(_.headOption),
         Duration.Inf) match {
-        case Some(x) => id
+        case Some(_) => id
         case _ =>
           logger.warn(
             s"Run id found in '$runIdFile' does not exist in summary, creating a new run")
@@ -191,22 +191,22 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
     qscript match {
       case q: MultiSampleQScript =>
         // Global level
-        for ((key, file) <- qscript.summaryFiles) addChecksum(file)
+        for ((_, file) <- qscript.summaryFiles) addChecksum(file)
 
-        for ((sampleName, sample) <- q.samples) {
+        for ((_, sample) <- q.samples) {
           // Sample level
-          for ((key, file) <- sample.summaryFiles) addChecksum(file)
-          for ((libName, lib) <- sample.libraries) {
+          for ((_, file) <- sample.summaryFiles) addChecksum(file)
+          for ((_, lib) <- sample.libraries) {
             // Library level
-            for ((key, file) <- lib.summaryFiles) addChecksum(file)
+            for ((_, file) <- lib.summaryFiles) addChecksum(file)
           }
         }
-      case q => for ((key, file) <- q.summaryFiles) addChecksum(file)
+      case q => for ((_, file) <- q.summaryFiles) addChecksum(file)
     }
 
     for (inputFile <- inputFiles) {
       inputFile.md5 match {
-        case Some(checksum) => {
+        case Some(checksum) =>
           val checkMd5 = new CheckChecksum
           checkMd5.inputFile = inputFile.file
           if (!SummaryQScript.md5sumCache.contains(inputFile.file))
@@ -216,7 +216,6 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
           checkMd5.jobOutputFile = new File(checkMd5.checksumFile.getParentFile,
                                             checkMd5.checksumFile.getName + ".check.out")
           add(checkMd5)
-        }
         case _ =>
       }
     }

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

@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.Input
 
 import scala.collection.mutable
 import scala.io.Source
-import scala.concurrent.Await
+import scala.concurrent.{Await, Future}
 import scala.concurrent.duration.Duration
 import scala.concurrent.ExecutionContext.Implicits.global
 
@@ -40,7 +40,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
   require(parent != null)
 
   /** To access qscript for this summary */
-  val qscript = parent
+  val qscript: SummaryQScript = parent
 
   @Input(doc = "deps", required = false)
   var deps: List[File] = Nil
@@ -62,28 +62,27 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
     val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     if (qscript == root) { // This initialize the database
       qscript match {
-        case s: MultiSampleQScript => s.initSummaryDb
+        case s: MultiSampleQScript => s.initSummaryDb()
         case t: SampleLibraryTag =>
           t.sampleId.foreach {
-            case sampleName =>
+            sampleName =>
               val sampleId = Await
                 .result(db.getSamples(name = Some(sampleName), runId = Some(qscript.summaryRunId))
-                          .map(_.headOption.map(_.id)),
-                        Duration.Inf)
+                  .map(_.headOption.map(_.id)),
+                  Duration.Inf)
                 .getOrElse {
                   Await.result(db.createOrUpdateSample(sampleName, qscript.summaryRunId),
-                               Duration.Inf)
+                    Duration.Inf)
                 }
               t.libId.foreach { libName =>
-                val libId = Await
-                  .result(db.getSamples(name = Some(libName),
-                                        runId = Some(qscript.summaryRunId),
-                                        sampleId = Some(sampleId))
-                            .map(_.headOption.map(_.id)),
-                          Duration.Inf)
+                Await.result(db.getSamples(name = Some(libName),