From 69b9397d9c9fdfc22129ec2050e401d08c9d54a4 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 28 Jan 2025 11:32:34 +0000 Subject: [PATCH] index should be emitted as either tbi or csi deepvariant will automatically switch to csi index for larger files, but these were not being picked up in the output, causing failure --- modules/nf-core/deepvariant/rundeepvariant/main.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/deepvariant/rundeepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf index aec18907646..b8119c464ec 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/main.nf +++ b/modules/nf-core/deepvariant/rundeepvariant/main.nf @@ -15,11 +15,11 @@ process DEEPVARIANT_RUNDEEPVARIANT { tuple val(meta5), path(par_bed) output: - tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf - tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: vcf_tbi - tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf - tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf + tuple val(meta), path("${prefix}.vcf.gz.{tbi,csi}") , emit: vcf_index + tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf + tuple val(meta), path("${prefix}.g.vcf.gz.{tbi,csi}") , emit: gvcf_index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when