Fixing code warnings

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

@@ -62,7 +62,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   var fastqcR1After: Fastqc = _
   var fastqcR2After: Fastqc = _
 
-  override def reportClass = {
+  override def reportClass: Some[FlexiprepReport] = {
     val flexiprepReport = new FlexiprepReport(this)
     flexiprepReport.outputDir = new File(outputDir, "report")
     flexiprepReport.summaryFile = summaryFile
@@ -74,6 +74,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
   /** Function that's need to be executed before the script is accessed */
   def init() {
+    paired = inputR2.isDefined
     if (inputR1 == null) Logging.addError("Missing input R1 on flexiprep module")
     if (sampleId == null || sampleId.isEmpty) Logging.addError("Missing sample ID on flexiprep module")
     if (libId == null || libId.isEmpty) Logging.addError("Missing library ID on flexiprep module")
@@ -147,10 +148,10 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     }
   }
 
-  def fastqR1Qc = if (paired)
+  def fastqR1Qc: File = if (paired)
     new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R1.qc.sync.fq.gz")
   else new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R1.qc.fq.gz")
-  def fastqR2Qc = if (paired)
+  def fastqR2Qc: Option[File] = if (paired)
     Some(new File(outputDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.R2.qc.sync.fq.gz"))
   else None
 
@@ -225,7 +226,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
         /** Must returns stats to store into summary */
         def summaryStats: Any = Map()
 
-        override def summaryDeps = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps
+        override def summaryDeps: List[File] = qcCmdR1.summaryDeps ::: qcCmdR2.summaryDeps ::: super.summaryDeps
       }
 
       pipe.deps ::= fastqcR1.output

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
-import nl.lumc.sasc.biopet.utils.{ Logging, textToSize }
+import nl.lumc.sasc.biopet.utils.textToSize
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -127,7 +127,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     })
 
   /** Settings to add to summary */
-  def summarySettings = Map(
+  def summarySettings: Map[String, Any] = Map(
     "skip_metrics" -> skipMetrics,
     "skip_flexiprep" -> skipFlexiprep,
     "skip_markduplicates" -> skipMarkduplicates,
@@ -137,7 +137,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     "number_of_chunks" -> (if (chunking) numberChunks.getOrElse(1) else None)
   ) ++ (if (root == null) Map("reference" -> referenceSummary) else Map())
 
-  override def reportClass = {
+  override def reportClass: Some[MappingReport] = {
     val mappingReport = new MappingReport(this)
     mappingReport.outputDir = new File(outputDir, "report")
     mappingReport.summaryFile = summaryFile
@@ -295,7 +295,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     addSummaryJobs()
   }
 
-  protected lazy val bam2wig = if (config("generate_wig", default = false)) {
+  protected lazy val bam2wig: Option[Bam2Wig] = if (config("generate_wig", default = false)) {
     Some(Bam2Wig(this, finalBamFile))
   } else None