From 457a3437b74fc3b594c853f25c5f1cf1d338c8a4 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Thu, 30 Jan 2020 10:43:35 +0100
Subject: [PATCH] Fix command section for Inspect.
---
centrifuge.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 2869d41..3f01d0e 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -187,7 +187,7 @@ task Inspect {
Map[String, String] outputOptions = {"fasta": "", "names": "--names", "summary": "--summary", "conversionTable": "--conversion-table", "taxonomyTree": "--taxonomy-tree", "nameTable": "--name-table", "sizeTable": "--size-table"}
- command {
+ command <<<
set -e
mkdir -p "$(dirname ~{outputPrefix})"
indexPath=~{sub(indexFiles[0], "\.[0-9]\.cf", "")}
@@ -198,7 +198,7 @@ task Inspect {
~{"--across " + across} \
$PWD/${indexBasename} \
> ~{outputPrefix + "/" + printOption}
- }
+ >>>
output {
File outputInspect = outputPrefix + "/" + printOption
--
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