From 27ec36f7e1f0e693174b3290af2f52294cac6a2d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Jun 2014 14:10:06 +0200
Subject: [PATCH] Fixed bug on single end runs
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 7eccc0230..15a304f5b 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -68,7 +68,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
if (paired) runTrimClip(outputFiles("fastq_input_R1"), outputFiles("fastq_input_R2"), outputDir)
else runTrimClip(outputFiles("fastq_input_R1"), outputDir)
- runFinalize(List(outputFiles("output_R1")), List(outputFiles("output_R2")))
+ runFinalize(List(outputFiles("output_R1")), if (outputFiles.contains("output_R2")) List(outputFiles("output_R2")) else List())
}
def runInitialFastqc() {
@@ -177,7 +177,7 @@ class Flexiprep(private var globalConfig: Config) extends QScript with BiopetQSc
}
def runFinalize(fastq_R1:List[File], fastq_R2:List[File]) {
- if (fastq_R1.length != fastq_R2.length) throw new IllegalStateException("R1 and R2 file number is not the same")
+ if (fastq_R1.length != fastq_R2.length && paired) throw new IllegalStateException("R1 and R2 file number is not the same")
var R1: File = ""
var R2: File = ""
if (fastq_R1.length == 1) {
--
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