From 23b324ea33f63cb4901fd66528f4ecead4cab0d5 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 24 Oct 2022 15:02:55 +0200
Subject: [PATCH] Copy reference to prevent problems
---
biowdl.wdl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/biowdl.wdl b/biowdl.wdl
index 7392983..fe49a6c 100644
--- a/biowdl.wdl
+++ b/biowdl.wdl
@@ -86,7 +86,7 @@ task IndexFastaFile {
command <<<
set -e
mkdir -p ~{outputDir}
- ln -s ~{inputFile} ~{outputFile}
+ cp ~{inputFile} ~{outputFile}
picard -Xmx~{javaXmx} \
-XX:ParallelGCThreads=1 \
CreateSequenceDictionary \
--
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