From 264c68bc7b164fa197cacd2270a32640c82ae70c Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 21 Feb 2018 13:09:03 +0100
Subject: [PATCH] proper dirname creation
---
common.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/common.wdl b/common.wdl
index 97731d4..7834088 100644
--- a/common.wdl
+++ b/common.wdl
@@ -34,8 +34,8 @@ task concatenateTextFiles {
String combinedFilePath
Boolean? unzip=false
command {
- mkdir -p ${combinedFilePath}
- rm -d ${combinedFilePath}
+ set -e -o pipefail
+ mkdir $(dirname ${combinedFilePath})
${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \
> ${combinedFilePath}
}
--
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