From b8414e7a3101cbac75f2fe39b515ccbd6434c582 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 20 Mar 2018 10:15:47 +0100
Subject: [PATCH] add precommand
---
mergecounts.wdl | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/mergecounts.wdl b/mergecounts.wdl
index de4bee4..ed5d5e7 100644
--- a/mergecounts.wdl
+++ b/mergecounts.wdl
@@ -1,4 +1,6 @@
task MergeCounts {
+ String? preCommand
+
Array[File] inputFiles
String outputFile
String idVar
@@ -6,6 +8,8 @@ task MergeCounts {
# Based on a script by Szymon Kielbasa/Ioannis Moustakas
command <<<
+ set -e -o pipefail
+ ${preCommand}
R --no-save --slave <<CODE > ${outputFile}
library(dplyr)
library(reshape2)
--
GitLab