Inspection round pipelines

carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -44,7 +44,7 @@ class CarpTest extends TestNGSuite with Matchers {
   }
 
   @DataProvider(name = "carpOptions")
-  def carpOptions = {
+  def carpOptions: Array[Array[Any]] = {
     val bool = Array(true, false)
 
     for (s1 <- bool; s2 <- bool; s3 <- bool; t <- bool; c <- bool)
@@ -103,7 +103,7 @@ class CarpTest extends TestNGSuite with Matchers {
   }
 
   // remove temporary run directory all tests in the class have been run
-  @AfterClass def removeTempOutputDir() = {
+  @AfterClass def removeTempOutputDir(): Unit = {
     dirs.filter(_.exists()).foreach { dir =>
       try {
         FileUtils.deleteDirectory(dir)
@@ -116,8 +116,8 @@ class CarpTest extends TestNGSuite with Matchers {
 }
 
 object CarpTest {
-  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)

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp

@@ -26,14 +26,14 @@
     val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)
     val settings = summary.getSettingsForLibraries(runId, "flexiprep", keyValues = Map(
     "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
-    settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
-    val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(false))
-    val clipCount = settings.count(_._2.getOrElse("skip_clip", None) == Some(false))
+    settings.count(_._2.getOrElse("skip_trim", None).contains(true))
+    val trimCount = settings.count(_._2.getOrElse("skip_trim", None).contains(false))
+    val clipCount = settings.count(_._2.getOrElse("skip_clip", None).contains(false))
     val librariesCount = libraries.size
 
     val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
-    summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
-    else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
+    summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None).contains(true)
+    else settings.count(_._2.getOrElse("paired", None).contains(true)) >= 1
 }#
 #if (showIntro)
     <br/>
@@ -118,7 +118,7 @@
         #for (sample <- samples.sortBy(_.name))
             #{
                 val sampleRowspan = {
-                libraries.filter(_.sampleId == sample.id).size +
+                libraries.count(_.sampleId == sample.id) +
                 settings.filter(_._1._1 == sample.id).count(_._2("paired").getOrElse(false) == true)
                 }
             }#
@@ -130,7 +130,7 @@
             #end
             </td>
             #for (lib <- libraries.filter(_.sampleId == sample.id))
-                #{ val paired = settings.filter(_._1._1 == sample.id).filter(_._1._2 == lib.id).head._2("paired") == Some(true) }#
+                #{ val paired = settings.filter(_._1._1 == sample.id).filter(_._1._2 == lib.id).head._2("paired").contains(true) }#
                 <td #if (paired == true) rowspan="2" #end>
                 #if (multisample)
                     <a href="${rootPath}Samples/${sample.name}/Libraries/${lib.name}/index.html">${lib.name}</a>

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp

@@ -21,25 +21,24 @@
     "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
     val run = Await.result(summary.getRuns(runId = Some(runId)).map(_.head), Duration.Inf)
 
-    val paired: Boolean = settings("paired") == Some(true)
-    val skipClip: Boolean = settings("skip_clip") == Some(true)
-    val skipTrim: Boolean = settings("skip_trim") == Some(true)
+    val paired: Boolean = settings("paired").contains(true)
+    val skipClip: Boolean = settings("skip_clip").contains(true)
+    val skipTrim: Boolean = settings("skip_trim").contains(true)
 
     def getPlot(read:String) = {
         val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), plot), Duration.Inf)
         file.collect {
-            case path => {
+            case path =>
                 val file = new File(run.outputDir + File.separator + path.path)
                 val newFile = new File(outputDir, read + "_" + file.getName)
                 if (file.exists()) FileUtils.copyFile(file, newFile)
                 newFile.getName
-            }
         }
     }
 
     def plotAvailable(read:String) = {
         val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), plot), Duration.Inf)
-        file.map(x => new File(run.outputDir + File.separator + x.path).exists()).getOrElse(false)
+        file.exists(x => new File(run.outputDir + File.separator + x.path).exists())
     }
 
 }#

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp

@@ -12,8 +12,8 @@
     <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>${run.outputDir}</td></tr>
-    <tr><th>Sample ID</th><td>${allSamples.filter(_.id == sampleId.get).headOption.map(_.name)}</td></tr>
-    <tr><th>Library ID</th><td>${allLibraries.filter(_.id == libId.get).headOption.map(_.name)}</td></tr>
+    <tr><th>Sample ID</th><td>${allSamples.find(_.id == sampleId.get).map(_.name)}</td></tr>
+    <tr><th>Library ID</th><td>${allLibraries.find(_.id == libId.get).map(_.name)}</td></tr>
 </tbody>
 </table>
 <br/>

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

@@ -25,14 +25,14 @@
     val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)
     val settings = summary.getSettingsForLibraries(runId, "flexiprep", keyValues = Map(
     "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
-    settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
-    val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(false))
-    val clipCount = settings.count(_._2.getOrElse("skip_clip", None) == Some(false))
+    settings.count(_._2.getOrElse("skip_trim", None).contains(true))
+    val trimCount = settings.count(_._2.getOrElse("skip_trim", None).contains(false))
+    val clipCount = settings.count(_._2.getOrElse("skip_clip", None).contains(false))
     val librariesCount = libraries.size
 
     val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
-        summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
-    else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
+        summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None).contains(true)
+    else settings.count(_._2.getOrElse("paired", None).contains(true)) >= 1
 }#
 
 #if (showIntro)
@@ -123,7 +123,7 @@
         #for (sample <- samples.sortBy(_.name))
             #{
                 val sampleRowspan = {
-                libraries.filter(_.sampleId == sample.id).size +
+                libraries.count(_.sampleId == sample.id) +
                  settings.filter(_._1._1 == sample.id).count(_._2("paired").getOrElse(false) == true)
                 }
             }#
@@ -135,7 +135,7 @@
             #end
             </td>
             #for (lib <- libraries.filter(_.sampleId == sample.id))
-                #{ val paired = settings.filter(_._1._1 == sample.id).filter(_._1._2 == lib.id).head._2("paired") == Some(true) }#
+                #{ val paired = settings.filter(_._1._1 == sample.id).filter(_._1._2 == lib.id).head._2("paired").contains(true) }#
                 <td #if (paired == true) rowspan="2" #end>
                 #if (multisample)
                     <a href="${rootPath}Samples/${sample.name}/Libraries/${lib.name}/index.html">${lib.name}</a>

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CheckValidateFastq.scala

@@ -32,7 +32,7 @@ class CheckValidateFastq extends InProcessFunction {
   var inputLogFile: File = _
 
   /** Exits whenever the input md5sum is not the same as the output md5sum */
-  def run: Unit = {
+  def run(): Unit = {
 
     val reader = Source.fromFile(inputLogFile)
     reader.getLines().foreach { line =>

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala

@@ -76,11 +76,10 @@ class Cutadapt(root: Configurable, fastqc: Fastqc)
           case (adapterSequence: String, adapterStats: Map[_, _]) =>
             seqToNameMap.get(adapterSequence) match {
               // adapter sequence is found by FastQC
-              case Some(adapterSeqName) => {
+              case Some(adapterSeqName) =>
                 Some(
                   adapterSeqName ->
                     Map("sequence" -> adapterSequence, "stats" -> adapterStats.toMap))
-              }
               // adapter sequence is clipped but not found by FastQC ~ should not happen since all clipped adapter
               // sequences come from FastQC
               case _ =>
@@ -88,14 +87,14 @@ class Cutadapt(root: Configurable, fastqc: Fastqc)
                   s"Adapter '$adapterSequence' is clipped but not found by FastQC in '$fastqInput'.")
             }
           // FastQC found no adapters
-          case otherwise =>
+          case _ =>
             logger.debug(s"No adapters found for summarizing in '$fastqInput'.")
             None
         }
       // "adapters" key not found ~ something went wrong in our part
       case _ =>
         throw new RuntimeException(
-          s"Required key '${adaptersStatsName}' not found in stats entry '${fastqInput}'.")
+          s"Required key '$adaptersStatsName' not found in stats entry '$fastqInput'.")
     }
     initStats.updated(adaptersStatsName, adapterCounts)
   }

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

@@ -288,7 +288,7 @@ object Fastqc {
     if (filename.endsWith(".fastq")) filename = filename.substring(0, filename.length - 6)
     fastqcCommand.getVersion.flatMap(SemanticVersion.getSemanticVersion) match {
       case Some(v) if v >= SemanticVersion(0, 11, 4) =>
-        if (filename.endsWith(".fq")) filename = filename.substring(0, filename.size - 3)
+        if (filename.endsWith(".fq")) filename = filename.substring(0, filename.length - 3)
       case _ =>
     }
     fastqcCommand.output = new File(outDir, filename + "_fastqc.zip")

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -50,7 +50,7 @@ class Flexiprep(val parent: Configurable)
   /** Make a final fastq files, by default only when flexiprep is the main pipeline */
   var keepQcFastqFiles: Boolean = config("keepQcFastqFiles", default = parent == null)
 
-  override def defaults = super.defaults ++ Map("max_threads" -> 4)
+  override def defaults: Map[String, Any] = super.defaults ++ Map("max_threads" -> 4)
 
   /** Returns files to store in summary */
   def summaryFiles: Map[String, File] = {

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CutadaptTest.scala

@@ -37,7 +37,7 @@ class CutadaptTest extends FastqcV0101Test {
     caExe
   }
 
-  @Test def testAdapterFound() = {
+  @Test def testAdapterFound(): Unit = {
     val cutadapt = testCutadaptInst
     val adapters = cutadapt.extractClippedAdapters(cutadaptOut)
     adapters.keys.size shouldBe 4
@@ -60,7 +60,7 @@ class CutadaptTest extends FastqcV0101Test {
     )
   }
 
-  @Test def testSummary() = {
+  @Test def testSummary(): Unit = {
     val cutadapt = testCutadaptInst
     val summary = cutadapt.summaryStats
 

flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala

@@ -35,14 +35,14 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
   // the file doesn't actually exist, we just need it so the outputDir value can be computed correctly
   private[flexiprep] val outputv0101: File = resourceFile("v0101.fq_fastqc.zip")
 
-  @Test def testOutputDir() = {
+  @Test def testOutputDir(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     fqc.outputDir shouldBe new File(resourceDir, "v0101.fq_fastqc")
   }
 
   @Test
-  def testGcDistro: Unit = {
+  def testGcDistro(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     val x = fqc.gcDistribution.get
@@ -54,7 +54,7 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
 
   }
 
-  @Test def testQcModules() = {
+  @Test def testQcModules(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     // 11 QC modules
@@ -67,7 +67,7 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
     fqc.qcModules.keySet should contain("Kmer Content")
   }
 
-  @Test def testSingleQcModule() = {
+  @Test def testSingleQcModule(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     fqc.qcModules("Basic Statistics").name should ===("Basic Statistics")
@@ -75,13 +75,13 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
     fqc.qcModules("Basic Statistics").lines.size shouldBe 8
   }
 
-  @Test def testEncoding() = {
+  @Test def testEncoding(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     fqc.encoding shouldBe "Sanger / Illumina 1.9"
   }
 
-  @Test def testFoundAdapter() = {
+  @Test def testFoundAdapter(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     fqc.contaminants = Option(resourceFile("fqc_contaminants_v0101.txt"))
@@ -102,7 +102,7 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
 
   }
 
-  @Test def testPerBaseSequenceQuality() = {
+  @Test def testPerBaseSequenceQuality(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
 
@@ -111,7 +111,7 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
     perBaseSequenceQuality.keys should contain("54-55")
   }
 
-  @Test def testPerBaseSequenceContent() = {
+  @Test def testPerBaseSequenceContent(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
 
@@ -120,7 +120,7 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
     perBaseSequenceContent.keys should contain("1")
   }
 
-  @Test def testSummaryStats() = {
+  @Test def testSummaryStats(): Unit = {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     val summary = fqc.summaryStats

gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.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/>

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/ExtractUnmappedReads.scala

@@ -43,7 +43,7 @@ class ExtractUnmappedReads(val parent: Configurable) extends QScript with Biopet
   }
 
   def fastqUnmappedR1 = new File(outputDir, s"$outputName.unmapped.R1.fq.gz")
-  def fastqUnmappedR2 =
+  def fastqUnmappedR2: Option[File] =
     if (paired) Some(new File(outputDir, s"$outputName.unmapped.R2.fq.gz"))
     else None
   def fastqUnmappedSingletons = new File(outputDir, s"$outputName.unmapped.singletons.fq.gz")

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala

@@ -30,7 +30,7 @@ import org.broadinstitute.gatk.queue.QScript
 class Gears(val parent: Configurable) extends QScript with MultiSampleQScript { qscript =>
   def this() = this(null)
 
-  override def reportClass = {
+  override def reportClass: Some[GearsReport] = {
     val gearsReport = new GearsReport(this)
     gearsReport.outputDir = new File(outputDir, "report")
     gearsReport.summaryDbFile = summaryDbFile
@@ -143,7 +143,8 @@ class Gears(val parent: Configurable) extends QScript with MultiSampleQScript {
 
       lazy val skipFlexiprep: Boolean = config("skip_flexiprep", default = false)
 
-      lazy val flexiprep = if (skipFlexiprep) None else Some(new Flexiprep(qscript))
+      lazy val flexiprep: Option[Flexiprep] =
+        if (skipFlexiprep) None else Some(new Flexiprep(qscript))
       flexiprep.foreach(_.sampleId = Some(sampleId))
       flexiprep.foreach(_.libId = Some(libId))
       flexiprep.foreach(_.inputR1 = inputR1)
@@ -155,7 +156,8 @@ class Gears(val parent: Configurable) extends QScript with MultiSampleQScript {
 
       val libraryGears: Boolean = config("library_gears", default = false)
 
-      lazy val gearsSingle = if (libraryGears) Some(new GearsSingle(qscript)) else None
+      lazy val gearsSingle: Option[GearsSingle] =
+        if (libraryGears) Some(new GearsSingle(qscript)) else None
 
       /** Function that add library jobs */
       protected def addJobs(): Unit = {
@@ -189,8 +191,6 @@ class Gears(val parent: Configurable) extends QScript with MultiSampleQScript {
     protected def addJobs(): Unit = {
       addPerLibJobs()
 
-      val flexipreps = libraries.values.map(_.flexiprep).toList
-
       val mergeR1: File = new File(sampleDir, s"$sampleId.R1.fq.gz")
       add(Zcat(qscript, libraries.values.map(_.qcR1).toList) | new Gzip(qscript) > mergeR1)
 

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala

@@ -132,7 +132,7 @@ object GearsKraken {
     val taxs: mutable.Map[String, Any] = mutable.Map()
 
     def addTax(map: Map[String, Any], path: List[String] = Nil): Unit = {
-      val name = map.get("name").getOrElse("noName").toString
+      val name = map.getOrElse("name", "noName").toString
       val x = path.foldLeft(taxs)(
         (a, b) =>
           if (a.contains(b)) a(b).asInstanceOf[mutable.Map[String, Any]]
@@ -144,20 +144,18 @@ object GearsKraken {
       if (!x.contains(name)) x += name -> mutable.Map[String, Any]()
 
       map
-        .get("children")
-        .getOrElse(List())
+        .getOrElse("children", List())
         .asInstanceOf[List[Any]]
         .foreach(x => addTax(x.asInstanceOf[Map[String, Any]], path ::: name :: Nil))
     }
 
     summaries.foreach { x =>
-      addTax(x._2.get("classified").getOrElse(Map()).asInstanceOf[Map[String, Any]])
+      addTax(x._2.getOrElse("classified", Map()).asInstanceOf[Map[String, Any]])
     }
 
     def getValue(sample: String, path: List[String], key: String) = {
       path
-        .foldLeft(
-          summaries(sample).get("classified").getOrElse(Map()).asInstanceOf[Map[String, Any]]) {
+        .foldLeft(summaries(sample).getOrElse("classified", Map()).asInstanceOf[Map[String, Any]]) {
           (b, a) =>
             b.getOrElse("children", List[Map[String, Any]]())
               .asInstanceOf[List[Map[String, Any]]]

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala

@@ -44,18 +44,18 @@ class GearsQiimeClosed(val parent: Configurable)
     )
   )
 
-  def init() = {
+  def init(): Unit = {
     require(fastqInput != null)
     require(sampleId.isDefined)
   }
 
   private var _otuMap: File = _
-  def otuMap = _otuMap
+  def otuMap: File = _otuMap
 
   private var _otuTable: File = _
-  def otuTable = _otuTable
+  def otuTable: File = _otuTable
 
-  def biopetScript() = {
+  def biopetScript(): Unit = {
 
     val splitLib = new SplitLibrariesFastq(this)
     splitLib.input :+= fastqInput
@@ -149,7 +149,7 @@ object GearsQiimeClosed {
     biom("data")
       .asInstanceOf[List[List[Any]]]
       .map { data =>
-        val row = data(0).asInstanceOf[Long]
+        val row = data.head.asInstanceOf[Long]
         val column = data(1).asInstanceOf[Long]
         val value = data(2).asInstanceOf[Long]
         val sample = samples(column.toInt).toString

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeOpen.scala

@@ -37,18 +37,18 @@ class GearsQiimeOpen(val parent: Configurable)
     )
   )
 
-  def init() = {
+  def init(): Unit = {
     require(fastqInput != null)
     require(sampleId.isDefined)
   }
 
   private var _otuMap: File = _
-  def otuMap = _otuMap
+  def otuMap: File = _otuMap
 
   private var _otuTable: File = _
-  def otuTable = _otuTable
+  def otuTable: File = _otuTable
 
-  def biopetScript() = {
+  def biopetScript(): Unit = {
 
     val splitLib = new SplitLibrariesFastq(this)
     splitLib.input :+= fastqInput

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala

@@ -58,11 +58,11 @@ class GearsQiimeRtax(val parent: Configurable)
     )
   )
 
-  def init() = {
+  def init(): Unit = {
     require(fastqR1 != null)
   }
 
-  def biopetScript() = {
+  def biopetScript(): Unit = {
 
     val slfR1 = new SplitLibrariesFastq(this)
     slfR1.input :+= fastqR1

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala

@@ -16,13 +16,14 @@ package nl.lumc.sasc.biopet.pipelines.gears
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.report.{ MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
+import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
 import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
+import nl.lumc.sasc.biopet.pipelines.gears
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
-import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{ NoLibrary, NoModule, SampleId }
+import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{NoLibrary, NoModule, SampleId}
 
-import scala.concurrent.{ Await, Future }
+import scala.concurrent.{Await, Future}
 import scala.concurrent.duration.Duration
 
 /**
@@ -40,7 +41,7 @@ object GearsReport extends MultisampleReportBuilder {
 
   def reportName = "Gears Report"
 
-  override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
+  override def extFiles: List[gears.GearsReport.ExtFile] = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
     .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
 
   def indexPage: Future[ReportPage] = Future {
@@ -51,29 +52,29 @@ object GearsReport extends MultisampleReportBuilder {
     val qiimeClosesOtuTable = summary.getFile(runId, "gears", key = "qiime_closed_otu_table")
     val qiimeOpenOtuTable = summary.getFile(runId, "gears", key = "qiime_open_otu_table")
 
-    val centrifugePage = (if (centrifugeExecuted) Some("Centrifuge analysis" -> Future.successful(ReportPage(List("Non-unique" ->
+    val centrifugePage = if (centrifugeExecuted) Some("Centrifuge analysis" -> Future.successful(ReportPage(List("Non-unique" ->
       Future.successful(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
         Map("summaryStatsTag" -> "centrifuge_report")
       )), Map()))), List(
       "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
         Map("summaryStatsTag" -> "centrifuge_unique_report")
       )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge")))))
-    else None)
+    else None
 
-    val krakenPage = (if (krakenExecuted) Some("Kraken analysis" -> Future.successful(ReportPage(List(), List(
+    val krakenPage = if (krakenExecuted) Some("Kraken analysis" -> Future.successful(ReportPage(List(), List(
       "Krona plot" -> Future.successful(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
       ))), Map())))
-    else None)
+    else None
 
-    val qiimeClosedPage = (if (qiimeClosesOtuTable.isDefined) Some("Qiime closed reference analysis" -> Future.successful(ReportPage(List(), List(
+    val qiimeClosedPage = if (qiimeClosesOtuTable.isDefined) Some("Qiime closed reference analysis" -> Future.successful(ReportPage(List(), List(
       "Krona plot" -> Future.successful(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
       ))), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeClosesOtuTable.get.path)))))
-    else None)
+    else None
 
-    val qiimeOpenPage = (if (qiimeOpenOtuTable.isDefined) Some("Qiime open reference analysis" -> Future.successful(ReportPage(List(), List(
+    val qiimeOpenPage = if (qiimeOpenOtuTable.isDefined) Some("Qiime open reference analysis" -> Future.successful(ReportPage(List(), List(
       "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
       )), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeOpenOtuTable.get.path)))))
-    else None)
+    else None
 
     ReportPage(
       List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List(
@@ -124,8 +125,6 @@ object GearsReport extends MultisampleReportBuilder {
 
   /** Library page */
   def libraryPage(sampleId: Int, libId: Int, args: Map[String, Any]): Future[ReportPage] = Future {
-    val sName = Await.result(summary.getSampleName(sampleId), Duration.Inf)
-    val lName = Await.result(summary.getLibraryName(libId), Duration.Inf)
 
     val flexiprepExecuted = Await.result(summary.getStatsSize(runId, "flexiprep", sample = sampleId, library = libId), Duration.Inf) >= 1
 

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala

@@ -30,7 +30,7 @@ class GearsSeqCount(val parent: Configurable)
 
   var fastqInput: File = _
 
-  def countFile = swapExt(outputDir, fastqInput, ".fastq.gz", ".counts.txt")
+  def countFile: File = swapExt(outputDir, fastqInput, ".fastq.gz", ".counts.txt")
 
   /** Init for pipeline */
   def init(): Unit = {}

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

@@ -51,7 +51,7 @@ class GearsSingle(val parent: Configurable)
   @Argument(required = false)
   var outputName: String = _
 
-  def getOutputName = {
+  def getOutputName: String = {
     if (outputName == null) {
       sampleId.getOrElse("noName") + libId.map("-" + _).getOrElse("")
     } else outputName
@@ -74,7 +74,7 @@ class GearsSingle(val parent: Configurable)
 
   }
 
-  lazy val krakenScript = {
+  lazy val krakenScript: Option[GearsKraken] = {
     if (config("gears_use_kraken", default = false)) {
       val kraken = new GearsKraken(this)
       kraken.outputDir = new File(outputDir, "kraken")
@@ -83,7 +83,7 @@ class GearsSingle(val parent: Configurable)
     } else None
   }
 
-  lazy val centrifugeScript = {
+  lazy val centrifugeScript: Option[GearsCentrifuge] = {
     if (config("gears_use_centrifuge", default = true)) {
       val centrifuge = new GearsCentrifuge(this)
       centrifuge.outputDir = new File(outputDir, "centrifuge")
@@ -92,7 +92,7 @@ class GearsSingle(val parent: Configurable)
     } else None
   }
 
-  lazy val qiimeRatx = {
+  lazy val qiimeRatx: Option[GearsQiimeRtax] = {
     if (config("gears_use_qiime_rtax", default = false)) {
       val qiimeRatx = new GearsQiimeRtax(this)
       qiimeRatx.outputDir = new File(outputDir, "qiime_rtax")
@@ -100,23 +100,23 @@ class GearsSingle(val parent: Configurable)
     } else None
   }
 
-  lazy val qiimeClosed =
+  lazy val qiimeClosed: Option[GearsQiimeClosed] =
     if (config("gears_use_qiime_closed", default = false)) Some(new GearsQiimeClosed(this))
     else None
-  lazy val qiimeOpen =
+  lazy val qiimeOpen: Option[GearsQiimeOpen] =
     if (config("gears_use_qiime_open", default = false)) Some(new GearsQiimeOpen(this)) else None
-  lazy val seqCount =
+  lazy val seqCount: Option[GearsSeqCount] =
     if (config("gears_use_seq_count", default = false)) Some(new GearsSeqCount(this)) else None
 
   /** Executed before running the script */
   def init(): Unit = {
-    if (fastqR1.isEmpty && !bamFile.isDefined)
+    if (fastqR1.isEmpty && bamFile.isEmpty)
       Logging.addError("Please specify fastq-file(s) or bam file")
     if (fastqR1.nonEmpty == bamFile.isDefined)
       Logging.addError("Provide either a bam file or a R1/R2 file")
     if (fastqR2.nonEmpty && fastqR1.size != fastqR2.size)
       Logging.addError("R1 and R2 has not the same number of files")
-    if (sampleId == null || sampleId == None)
+    if (sampleId == null || sampleId.isEmpty)
       Logging.addError("Missing sample ID on GearsSingle module")
 
     if (!skipFlexiprep) {
@@ -145,7 +145,7 @@ class GearsSingle(val parent: Configurable)
     } else bamFile.foreach(inputFiles :+= InputFile(_))
   }
 
-  override def reportClass = {
+  override def reportClass: Some[GearsSingleReport] = {
     val gears = new GearsSingleReport(this)
     gears.outputDir = new File(outputDir, "report")
     gears.summaryDbFile = summaryDbFile

gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala

@@ -15,6 +15,7 @@
 package nl.lumc.sasc.biopet.pipelines.gears
 
 import nl.lumc.sasc.biopet.core.report._