From df5c19a1a68ddf457c93fc811d9c337655dcb75f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 16 Apr 2021 18:36:03 +0200
Subject: [PATCH] gatk3: fix high_confidence_snp_filter call
---
src/nf_modules/gatk3/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/gatk3/main.nf b/src/nf_modules/gatk3/main.nf
index cedf9446..35a1ab7a 100644
--- a/src/nf_modules/gatk3/main.nf
+++ b/src/nf_modules/gatk3/main.nf
@@ -97,8 +97,8 @@ gatk3 -T SelectVariants \
"""
}
-high_confidence_snp_filter = "(QD < 2.0) || (FS > 60.0) || (MQ < 40.0) || (MQRankSum < -12.5) || (ReadPosRankSum < -8.0) || (SOR > 4.0)"
-params.high_confidence_snp = "--filterExpression \"${high_confidence_snp_filter}\" --filterName \"basic_snp_filter\""
+params.high_confidence_snp_filter = "(QD < 2.0) || (FS > 60.0) || (MQ < 40.0) || (MQRankSum < -12.5) || (ReadPosRankSum < -8.0) || (SOR > 4.0)"
+params.high_confidence_snp = "--filterExpression \"${params.high_confidence_snp_filter}\" --filterName \"basic_snp_filter\""
params.high_confidence_snp_out = ""
process high_confidence_snp {
container = "${container_url}"
@@ -129,8 +129,8 @@ gatk3 -T VariantFiltration \
"""
}
-high_confidence_indel_filter = "QD < 3.0 || FS > 200.0 || ReadPosRankSum < -20.0 || SOR > 10.0"
-params.high_confidence_indels = "--filterExpression \"${high_confidence_indel_filter}\" --filterName \"basic_indel_filter\""
+params.high_confidence_indel_filter = "QD < 3.0 || FS > 200.0 || ReadPosRankSum < -20.0 || SOR > 10.0"
+params.high_confidence_indels = "--filterExpression \"${params.high_confidence_indel_filter}\" --filterName \"basic_indel_filter\""
params.high_confidence_indels_out = ""
process high_confidence_indels {
container = "${container_url}"
--
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