From b5fa57a6e5f42b2f113ded19b5203e6de31ac496 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Mar 2021 11:02:13 +0100
Subject: [PATCH] gatk4: update SelectVariants options
---
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 0b941592..0a4bd9c4 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -38,7 +38,7 @@ process filter_snp {
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \
-V ${vcf} \
- -selectType SNP \
+ -select-type SNP \
-O ${file_id}_snp.vcf
"""
}
@@ -59,7 +59,7 @@ process filter_indels {
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \
-V ${vcf} \
- -selectType INDEL \
+ -select-type INDEL \
-O ${file_id}_indel.vcf
"""
}
@@ -216,7 +216,7 @@ process select_variants_snp {
gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
-R ${fasta} \
-V ${vcf} \
- -selectType SNP \
+ -select-type SNP \
-O ${file_id}_joint_snp.vcf
"""
}
@@ -237,7 +237,7 @@ process select_variants_indels {
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \
-V ${vcf} \
- -selectType INDEL \
+ -select-type INDEL \
-O ${file_id}_joint_indel.vcf
"""
}
--
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