From 106ff35f06c8529fac3f914fbe83595794ba15c1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Mar 2021 15:33:27 +0100
Subject: [PATCH] gatk4: fix gvcf_genotyping variable :199
---
src/nf_modules/gatk4/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 737c1ea4..22efa0e0 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -196,7 +196,7 @@ process gvcf_genotyping {
gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
-R ${fasta} \
-V ${gvcf} \
- -O ${bam.simpleName}_joint.vcf.gz
+ -O ${gvcf.simpleName}_joint.vcf.gz
"""
}
--
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