From 9b7c5ff9ec2a11155031f18167ce08cba943eac3 Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Wed, 15 Aug 2018 15:32:24 +0200
Subject: [PATCH] iFixed R2 arg
---
cutadapt.wdl | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 8b07344..e89531b 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -61,10 +61,12 @@ task Cutadapt {
String? reportPath
}
+ String read2outputarg = if (defined(read2output)) then "mkdir -p $(dirname " + read2output + ")" else ""
+
command {
set -e -o pipefail
~{"mkdir -p $(dirname " + read1output + ")"}
- ~{"mkdir -p $(dirname " + read2output + ")"}
+ ~{read2outputarg}
~{"mkdir -p $(dirname " + reportPath + ")"}
~{preCommand}
cutadapt \
--
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