From ad62f7150a4ee1b72480516be152c518f3376b16 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 May 2018 12:54:50 +0200
Subject: [PATCH] only create link when output dir is given
---
bwa.wdl | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/bwa.wdl b/bwa.wdl
index 5839a9c..ffa4231 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -40,7 +40,10 @@ task index {
set -e -o pipefail
${"mkdir -p " + outputDir}
${preCommand}
- ln -sf ${fasta} ${outputDir + "/"}${fastaFilename}
+ if [[ ! '${outputDir}' = '' ]]
+ then
+ ln -sf ${fasta} ${outputDir + "/"}${fastaFilename}
+ fi
bwa index \
${"-a " + constructionAlgorithm} \
${"-b" + blockSize} \
--
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