diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala index 608afa3c0945e05e5c669ba8737393ea13109da3..f8cddedfd99753443787f858e294258cea292665 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala +++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala @@ -28,15 +28,15 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w private lazy val forwardPrimers: List[String] = config("forward_primers", default = Nil) private lazy val reversePrimers: List[String] = config("reverse_primers", default = Nil) - def combinedFastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty) + def combinedFastq: File = if ((forwardPrimers ::: reversePrimers).nonEmpty) swapExt(outputDir, flash.combinedFastq, ".fastq.gz", ".clip.fastq.gz") else flash.combinedFastq - def notCombinedR1Fastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty) + def notCombinedR1Fastq: File = if ((forwardPrimers ::: reversePrimers).nonEmpty) swapExt(outputDir, flash.notCombinedR1, ".fastq.gz", ".clip.fastq.gz") else flash.notCombinedR1 - def notCombinedR2Fastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty) + def notCombinedR2Fastq: File = if ((forwardPrimers ::: reversePrimers).nonEmpty) swapExt(outputDir, flash.notCombinedR2, ".fastq.gz", ".clip.fastq.gz") else flash.notCombinedR2