From a3352431bffb16b3f0d2ea243aa5c46a92f7a781 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 6 Mar 2018 10:17:07 +0100
Subject: [PATCH] add gzip
---
poretools.wdl | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/poretools.wdl b/poretools.wdl
index 5f96160..19ba43f 100644
--- a/poretools.wdl
+++ b/poretools.wdl
@@ -1,5 +1,5 @@
task fastq {
- Array[File] files
+ Array[File]+ files
String outputFile
String? preCommand
String? type
@@ -10,6 +10,7 @@ task fastq {
Boolean? highQuality
Boolean? normalQuality
String? group
+ Boolean? gzip = true
command {
set -e -o pipefail
mkdir -p $(dirname ${outputFile})
@@ -24,7 +25,7 @@ task fastq {
${if highQuality then "--high-quality" else ""} \
${if normalQuality then "--normal-quality" else ""} \
${"--group " + group} \
- ${sep=" " files} > ${outputFile}
+ ${sep=" " files} ${if gzip then "| gzip " else ""}> ${outputFile}
}
output {
--
GitLab