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greatly simplify syntax (#1121)

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Maxime U. Garcia 2021-12-07 11:18:12 +01:00 committed by GitHub
parent 6510a7ff4f
commit 3b366c7c6a
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4 changed files with 8 additions and 12 deletions
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8
modules/ensemblvep/main.nf
View file

@ -3,11 +3,9 @@ process ENSEMBLVEP {
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null) conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null)
container "${ task.ext.container_tag ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
"nfcore/vep:${task.ext.container_tag}" : 'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }"
'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' :
'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

8
modules/snpeff/main.nf
View file

@ -3,11 +3,9 @@ process SNPEFF {
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::snpeff=5.0" : null) conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
container "${ task.ext.container_tag ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
"nfcore/snpeff:${task.ext.container_tag}" : 'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

2
tests/modules/ensemblvep/nextflow.config
View file

@ -3,7 +3,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: ENSEMBLVEP { withName: ENSEMBLVEP {
ext.container_tag = '104.3.WBcel235' container = 'nfcore/vep:104.3.WBcel235'
} }
} }

2
tests/modules/snpeff/nextflow.config
View file

@ -3,7 +3,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: SNPEFF { withName: SNPEFF {
ext.container_tag = '5.0.WBcel235' container = 'nfcore/snpeff:5.0.WBcel235'
} }
} }