Fixed summary

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

@@ -29,7 +29,8 @@ class ExtractUnmappedReads(val root: Configurable) extends QScript with BiopetQS
   }
 
   def fastqUnmappedR1 = new File(outputDir, s"$outputName.unmapped.R1.fq.gz")
-  def fastqUnmappedR2 = new File(outputDir, s"$outputName.unmapped.R2.fq.gz")
+  def fastqUnmappedR2 = 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")
 
   def biopetScript(): Unit = {
@@ -48,7 +49,7 @@ class ExtractUnmappedReads(val root: Configurable) extends QScript with BiopetQS
     samToFastq.input = samtoolsViewSelectUnmapped.output
     samToFastq.fastqR1 = fastqUnmappedR1
     if (paired) {
-      samToFastq.fastqR2 = fastqUnmappedR2
+      samToFastq.fastqR2 = fastqUnmappedR2.get
       samToFastq.fastqUnpaired = fastqUnmappedSingletons
     }
     samToFastq.isIntermediate = !config("keep_unmapped_fastq", default = false).asBoolean

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

@@ -97,7 +97,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
 
   /** Statistics shown in the summary file */
   def summaryFiles: Map[String, File] = outputFiles + ("input_R1" -> fastqR1) ++ (fastqR2 match {
-    case Some(file) => Map("input_R1" -> file)
+    case Some(file) => Map("input_R2" -> file)
     case _          => Map()
   })
 }

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

@@ -97,7 +97,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
         extract.bamFile = bam
         extract.outputName = outputName
         add(extract)
-        executeFlexiprep(extract.fastqUnmappedR1, Some(extract.fastqUnmappedR2))
+        executeFlexiprep(extract.fastqUnmappedR1, extract.fastqUnmappedR2)
       case _ => throw new IllegalArgumentException("Missing input files")
     }
 
@@ -159,6 +159,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
   def summaryFiles: Map[String, File] = Map.empty ++
     (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
     (if (fastqR1.isDefined) Map("input_R1" -> fastqR1.get) else Map()) ++
+    (if (fastqR2.isDefined) Map("input_R2" -> fastqR2.get) else Map()) ++
     outputFiles
 }