From 8afdecfc69a3f54f773581497dab9efe3916b6e7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 20 Jan 2016 19:17:52 +0100
Subject: [PATCH] Fix compile issue
---
.../lumc/sasc/biopet/pipelines/gears/CombineReads.scala | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
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 66abc4caf..af2f46af6 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
@@ -50,10 +50,10 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
if ((forwardPrimers ::: reversePrimers).nonEmpty) {
val cutadapt = new Cutadapt(this)
- cutadapt.fastq_input = flash.combinedFastq
- cutadapt.fastq_output = this.combinedFastq
- cutadapt.stats_output = swapExt(outputDir, cutadapt.fastq_output, ".fastq.gz", ".stats")
- (forwardPrimers ::: reversePrimers).foreach(cutadapt.opt_anywhere += _)
+ cutadapt.fastqInput = flash.combinedFastq
+ cutadapt.fastqOutput = this.combinedFastq
+ cutadapt.statsOutput = swapExt(outputDir, cutadapt.fastqOutput, ".fastq.gz", ".stats")
+ (forwardPrimers ::: reversePrimers).foreach(cutadapt.anywhere += _)
add(cutadapt)
addSummarizable(cutadapt, "cutadapt")
}
--
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