From 3eccb5b72d896fedff0974579b3eb1b6ab291035 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 5 Jun 2020 13:38:16 +0200
Subject: [PATCH] fix typo and use newer version of GATK
---
gatk.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 88904be..c00af93 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1575,15 +1575,15 @@ task VariantEval {
String javaXmx = "4G"
# TODO: Refine estimate. For now 4 minutes per GB of input.
Int timeMinutes = ceil(size(flatten([evalVcfs, comparisonVcfs]), "G") * 4)
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.7.0--py38_0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
gatk --java-options '-Xmx~{javaXmx} -XX:ParallelGCThreads=1' \
- VariantFiltration \
- -O ~{outputPath} \
+ VariantEval \
+ --output ~{outputPath} \
~{true="--eval" false="" length(evalVcfs) > 0} ~{sep=" --eval " evalVcfs} \
~{true="--comparison" false="" length(comparisonVcfs) > 0} ~{sep=" --comparison " comparisonVcfs} \
~{"-R " + referenceFasta} \
--
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