From e3b5bc659ce900d8568fc79f97736ad3b80304a9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 12 Mar 2021 11:16:56 +0100
Subject: [PATCH] gatk4: make gvcf_genotyping emit vcf.gz files
---
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 ef296cb8..44049069 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -189,14 +189,14 @@ process gvcf_genotyping {
tuple val(file_id), path(gvcf)
tuple val(ref_id), path(fasta), path(fai), path(dict)
output:
- tuple val(file_id), path("*.vcf"), emit: vcf
+ tuple val(file_id), path("*.vcf.gz"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
-R ${fasta} \
-V ${gvcf} \
- -O ${file_id}_joint.vcf
+ -O ${file_id}_joint.vcf.gz
"""
}
--
GitLab