Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-718

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')

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -31,7 +31,7 @@ class Bam2Wig(val parent: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)
 
   @Input(doc = "Input bam file", required = true)
-  var bamFile: File = null
+  var bamFile: File = _
 
   def init(): Unit = {
     inputFiles :+= new InputFile(bamFile)

bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala

@@ -32,7 +32,7 @@ class BamToChromSizesTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testChromSizes: Unit = {
+  def testChromSizes(): Unit = {
     val bamFile = new File(resourcePath("/empty.bam"))
     val bamToChromSizes = new BamToChromSizes(null)
     bamToChromSizes.bamFile = bamFile

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp

@@ -13,8 +13,8 @@
     <tr><th>Version</th><td>${run.version}</td></tr>
     <tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
     <tr><th>Output directory</th><td>${run.outputDir}</td></tr>
-    <tr><th>Sample</th><td>${allSamples.filter(_.id == sampleId.get).headOption.map(_.name)}</td></tr>
-    <tr><th>Library</th><td>${allLibraries.filter(_.id == libId.get).headOption.map(_.name)}</td></tr>
+    <tr><th>Sample</th><td>${allSamples.find(_.id == sampleId.get).map(_.name)}</td></tr>
+    <tr><th>Library</th><td>${allLibraries.find(_.id == libId.get).map(_.name)}</td></tr>
 </tbody>
 </table>
 <br/>

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -48,7 +48,7 @@ class BamMetrics(val parent: Configurable)
   override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))
 
   /** returns files to store in summary */
-  def summaryFiles =
+  def summaryFiles: Map[String, File] =
     Map("reference" -> referenceFasta(), "input_bam" -> inputBam) ++
       ampliconBedFile.map("amplicon" -> _).toMap ++
       ampliconBedFile.map(x => "roi_" + x.getName.stripSuffix(".bed") -> x).toMap
@@ -58,7 +58,7 @@ class BamMetrics(val parent: Configurable)
     Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
         "roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
 
-  override def reportClass = {
+  override def reportClass: Some[BammetricsReport] = {
     val bammetricsReport = new BammetricsReport(this)
     bammetricsReport.outputDir = new File(outputDir, "report")
     bammetricsReport.summaryDbFile = summaryDbFile

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -487,7 +487,7 @@ object BammetricsReport extends ReportBuilder {
   }
 
   def writeTableToTsv(tsvFile: File, table: Map[String, Array[Any]], firstColumn: String): Unit = {
-    require(table.map(_._2.size).toList.distinct.size == 1,
+    require(table.map(_._2.length).toList.distinct.size == 1,
             "Not all values has the same number or rows")
     val keys = table.keys.filterNot(_ == firstColumn).toList.sorted
     val writer = new PrintWriter(tsvFile)

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -44,7 +44,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   }
 
   @DataProvider(name = "bammetricsOptions")
-  def bammetricsOptions = {
+  def bammetricsOptions: Array[Array[AnyVal]] = {
     val rois = Array(0, 1, 2, 3)
     val bool = Array(true, false)
 
@@ -57,7 +57,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   private var dirs: List[File] = Nil
 
   @Test(dataProvider = "bammetricsOptions")
-  def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = {
+  def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean): Unit = {
     val outputDir = Files.createTempDir()
     dirs :+= outputDir
     val map = ConfigUtils.mergeMaps(Map("output_dir" -> outputDir,
@@ -74,8 +74,6 @@ class BamMetricsTest extends TestNGSuite with Matchers {
     bammetrics.libId = Some("1")
     bammetrics.script()
 
-    var regions: Int = rois + (if (amplicon) 1 else 0)
-
     bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (wgs) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
@@ -86,13 +84,13 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   }
 
   // remove temporary run directory all tests in the class have been run
-  @AfterClass def removeTempOutputDir() = {
+  @AfterClass def removeTempOutputDir(): Unit = {
     dirs.foreach(FileUtils.deleteDirectory)
   }
 }
 
 object BamMetricsTest {
-  val inputDir = Files.createTempDir()
+  val inputDir: File = Files.createTempDir()
 
   val bam = new File(inputDir, "bla.bam")
   Files.touch(bam)
@@ -100,7 +98,7 @@ object BamMetricsTest {
   Files.touch(ampliconBed)
 
   def roi(i: Int): File = {
-    val roi = new File(inputDir, s"roi${i}.bed")
+    val roi = new File(inputDir, s"roi$i.bed")
     Files.touch(roi)
     roi
   }

basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -42,7 +42,7 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
 
   def variantcallers = List("unifiedgenotyper")
 
-  val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
+  val numBoot: Int = config("boot_runs", default = 100, namespace = "raxml").asInt
 
   override def defaults = Map(
     "ploidy" -> 1,

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -48,7 +48,7 @@ class BastyTest extends TestNGSuite with Matchers {
   }
 
   @DataProvider(name = "bastyOptions")
-  def bastyOptions = {
+  def bastyOptions: Array[Array[Any]] = {
     for (s1 <- sample1; s2 <- sample2) yield Array("", s1, s2)
   }
 
@@ -114,7 +114,7 @@ class BastyTest extends TestNGSuite with Matchers {
                                                                                    numberSamples
                                                                                  else 0)
       pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration)
-                                                                             (numberLibs * 2)
+                                                                             numberLibs * 2
                                                                            else 0)
       pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration)
                                                                        numberLibs
@@ -125,7 +125,7 @@ class BastyTest extends TestNGSuite with Matchers {
       pipeline.summaryFiles shouldBe Map()
 
       pipeline.samples foreach {
-        case (sampleId, sample) =>
+        case (_, sample) =>
           sample.summarySettings shouldBe Map()
           sample.summaryFiles.get("variants_fasta") should not be None
           sample.summaryFiles.get("consensus_fasta") should not be None
@@ -135,7 +135,7 @@ class BastyTest extends TestNGSuite with Matchers {
           sample.summaryFiles.get("snps_only_consensus_variants_fasta") should not be None
           sample.summaryStats shouldBe Map()
           sample.libraries.foreach {
-            case (libId, lib) =>
+            case (_, lib) =>
               lib.summarySettings shouldBe Map()
               lib.summaryFiles shouldBe Map()
               lib.summaryStats shouldBe Map()
@@ -154,14 +154,14 @@ class BastyTest extends TestNGSuite with Matchers {
   }
 
   // remove temporary run directory all tests in the class have been run
-  @AfterClass def removeTempOutputDir() = {
+  @AfterClass def removeTempOutputDir(): Unit = {
     dirs.foreach(FileUtils.deleteDirectory)
   }
 }
 
 object BastyTest {
-  def outputDir = Files.createTempDir()
-  val inputDir = Files.createTempDir()
+  def outputDir: File = Files.createTempDir()
+  val inputDir: File = Files.createTempDir()
 
   def inputTouch(name: String): String = {
     val file = new File(inputDir, name)

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 {