diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf index 78f2712c..e3d0c286 100644 --- a/modules/ensemblvep/main.nf +++ b/modules/ensemblvep/main.nf @@ -3,11 +3,9 @@ process ENSEMBLVEP { label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null) - container "${ task.ext.container_tag ? - "nfcore/vep:${task.ext.container_tag}" : - workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' : - 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' : + 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf index 9847c513..6248fee3 100644 --- a/modules/snpeff/main.nf +++ b/modules/snpeff/main.nf @@ -3,11 +3,9 @@ process SNPEFF { label 'process_medium' conda (params.enable_conda ? "bioconda::snpeff=5.0" : null) - container "${ task.ext.container_tag ? - "nfcore/snpeff:${task.ext.container_tag}" : - workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' : - 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' : + 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }" input: tuple val(meta), path(vcf) diff --git a/tests/modules/ensemblvep/nextflow.config b/tests/modules/ensemblvep/nextflow.config index 717fcae9..f13d62e9 100644 --- a/tests/modules/ensemblvep/nextflow.config +++ b/tests/modules/ensemblvep/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: ENSEMBLVEP { - ext.container_tag = '104.3.WBcel235' + container = 'nfcore/vep:104.3.WBcel235' } } diff --git a/tests/modules/snpeff/nextflow.config b/tests/modules/snpeff/nextflow.config index 3b094eed..f4042ab9 100644 --- a/tests/modules/snpeff/nextflow.config +++ b/tests/modules/snpeff/nextflow.config @@ -3,7 +3,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } withName: SNPEFF { - ext.container_tag = '5.0.WBcel235' + container = 'nfcore/snpeff:5.0.WBcel235' } }