From d619ed187c741316efe435433f3bf72a6130bc1b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 4 May 2018 15:49:56 +0200
Subject: [PATCH] add extra operater to concatenateTextFiles
---
common.wdl | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/common.wdl b/common.wdl
index 4acd8bd..2ac9cb9 100644
--- a/common.wdl
+++ b/common.wdl
@@ -51,12 +51,13 @@ task concatenateTextFiles {
Array[File] fileList
String combinedFilePath
Boolean? unzip=false
+ Boolean? zip=false
command {
set -e -o pipefail
${"mkdir -p $(dirname " + combinedFilePath + ")"}
${true='zcat' false= 'cat' unzip} ${sep=' ' fileList} \
- > ${combinedFilePath}
+ ${true="| gzip -c" false="" zip} > ${combinedFilePath}
}
output {
--
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