From 6d69470a8fd7128f8daac9aa32e700e986695123 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Mar 2021 11:19:56 +0100
Subject: [PATCH] gatk4: fix VariantFiltration params
---
src/nf_modules/gatk4/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 0a4bd9c4..82784453 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -82,8 +82,8 @@ process high_confidence_snp {
gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-R ${fasta} \
-V ${vcf} \
- --filterExpression "${high_confidence_snp_filter}" \
- --filterName "basic_snp_filter" \
+ --filter-expression "${high_confidence_snp_filter}" \
+ --filter-name "basic_snp_filter" \
-O ${file_id}_filtered_snp.vcf
"""
}
@@ -106,8 +106,8 @@ process high_confidence_indels {
gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-R ${fasta} \
-V ${vcf} \
- --filterExpression "${high_confidence_indel_filter}" \
- --filterName "basic_indel_filter" \
+ --filter-expression "${high_confidence_indel_filter}" \
+ --filter-name "basic_indel_filter" \
-O ${file_id}_filtered_indel.vcf
"""
}
--
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