From 481a7a969498254c79f96bf15ae47d0923320f23 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Feb 2015 17:52:17 +0100
Subject: [PATCH] Skip extractIfNeeded on R2 when not paired
---
.../nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index e1080ff0f..74779fc20 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -146,8 +146,10 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
chunks += (chunkDir -> (removeGz(chunkDir + input_R1.getName),
if (paired) removeGz(chunkDir + input_R2.get.getName) else ""))
}
- else chunks += (outputDir -> (flexiprep.extractIfNeeded(input_R1, flexiprep.outputDir),
- flexiprep.extractIfNeeded(input_R2.getOrElse(null), flexiprep.outputDir)))
+ else chunks += (outputDir -> (
+ flexiprep.extractIfNeeded(input_R1, flexiprep.outputDir),
+ if (paired) flexiprep.extractIfNeeded(input_R2.get, flexiprep.outputDir) else "")
+ )
if (chunking) {
val fastSplitter_R1 = new FastqSplitter(this)
--
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