From 4e4f4bf8765525a57faf13311cb74f14071f808a Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 9 May 2018 12:56:05 +0200
Subject: [PATCH] fix bwa index output file error

---
 bwa.wdl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bwa.wdl b/bwa.wdl
index ffa4231..2845c32 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -35,6 +35,7 @@ task index {
     Int? blockSize
     String? outputDir
     String fastaFilename = basename(fasta)
+    String outputFile = if (defined(outputDir)) then outputDir + "/" + fastaFilename else fasta
 
     command {
         set -e -o pipefail
@@ -47,7 +48,7 @@ task index {
         bwa index \
         ${"-a " + constructionAlgorithm} \
         ${"-b" + blockSize} \
-        ${outputDir + "/"}${fastaFilename}
+        ${outputFile}
     }
 
     output {
-- 
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