From 92c7e92334726396ce1ac9127c3513c86cd33cd0 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Wed, 15 Apr 2020 14:30:23 +0200
Subject: [PATCH] Update brackets.
---
isoseq3.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/isoseq3.wdl b/isoseq3.wdl
index 474709a..10d87bb 100644
--- a/isoseq3.wdl
+++ b/isoseq3.wdl
@@ -35,7 +35,7 @@ task Refine {
String dockerImage = "quay.io/biocontainers/isoseq3:3.3.0--0"
}
- command <<<
+ command {
set -e
mkdir -p "~{outputDir}"
isoseq3 refine \
@@ -47,7 +47,7 @@ task Refine {
~{inputBamFile} \
~{primerFile} \
"~{outputDir}/~{outputNamePrefix}.bam"
- >>>
+ }
output {
File outputFLNCfile = outputDir + "/" + outputNamePrefix + ".bam"
--
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