diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf index 737c1ea43daec71296067d4ee9eb0345dc8fca25..22efa0e0c0253f9f6a57db529d018c7978a93568 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 """ }