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Commit 61da844e authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed output files

parent 07c60ba5
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......@@ -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
......
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