From 93c9b2e9c90b34c358d41013bfac4806ffb10db9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Mar 2021 10:54:20 +0100
Subject: [PATCH] gatk4: fix SelectVariants cmd (remove -T)
---
src/nf_modules/gatk4/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 6a19e272..0b941592 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -56,7 +56,7 @@ process filter_indels {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
-gatk --java-options "-Xmx${xmx_memory}G"-T SelectVariants \
+gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \
-V ${vcf} \
-selectType INDEL \
@@ -79,7 +79,7 @@ process high_confidence_snp {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
-gatk --java-options "-Xmx${xmx_memory}G"-T VariantFiltration \
+gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-R ${fasta} \
-V ${vcf} \
--filterExpression "${high_confidence_snp_filter}" \
--
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