From 4a42403fb4bf27ba21f63b99c7cb75f9d13adfeb Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 8 Nov 2022 16:33:30 +0100
Subject: [PATCH] Fallback to copying when hardlinking does not work
---
samtools.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index df712e5..587a53f 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -332,7 +332,7 @@ task Index {
if [ ! -f ~{outputPath} ]
then
mkdir -p "$(dirname ~{outputPath})"
- ln ~{bamFile} ~{outputPath}
+ ln ~{bamFile} ~{outputPath} || cp ~{bamFile} ~{outputPath}
fi
samtools index ~{outputPath} ~{bamIndexPath}
'
@@ -531,7 +531,7 @@ task Tabix {
mkdir -p "$(dirname ~{outputFilePath})"
if [ ! -f ~{outputFilePath} ]
then
- ln ~{inputFile} ~{outputFilePath}
+ ln ~{inputFile} ~{outputFilePath} || cp ~{inputFile} ~{outputFilePath}
fi
tabix ~{outputFilePath} -p ~{type}
}
--
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