From 631b5dfa75c053afb0cd97be154bd34534e98167 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 17 Jul 2020 09:27:27 +0200
Subject: [PATCH] fix view task
---
bcftools.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/bcftools.wdl b/bcftools.wdl
index e60142d..b99a8cf 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -37,9 +37,9 @@ task View {
set -e
mkdir -p "$(dirname ~{outputPath})"
bcftools view \
- ~{inputFile} -o ~{outputPath} \
+ -o ~{outputPath} \
-O ~{outputType} \
- -l ~{compressionLevel}
+ -l ~{compressionLevel} \
~{inputFile}
bcftools index --tbi ~{outputPath}
--
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