From 71f30e0260f75ad90aaa2320b8f8ba3abdfdfff4 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 9 May 2018 13:07:35 +0200
Subject: [PATCH] fix output of bwa index task
---
bwa.wdl | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 2845c32..90b017f 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -52,8 +52,7 @@ task index {
}
output {
- File indexBase = if (defined(outputDir)) then select_first([outputDir]) + "/" + fastaFilename else fastaFilename
- File indexedFasta = indexBase
+ File indexedFasta = outputFile
Array[File] indexFiles = [indexBase + ".bwt",indexBase + ".pac",indexBase + ".sa",indexBase + ".amb",indexBase + ".ann"]
}
parameter_meta {
--
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