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feat: add meta.id tag (#1116)

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* feat: add meat.id tag

* fix: actually call the right container for singularity
This commit is contained in:
Maxime U. Garcia 2021-12-07 10:30:35 +01:00 committed by GitHub
parent 7006699ff8
commit 6510a7ff4f
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2 changed files with 10 additions and 8 deletions
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9
modules/ensemblvep/main.nf
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@ -1,12 +1,13 @@
process ENSEMBLVEP { process ENSEMBLVEP {
tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null) conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ task.ext.container_tag ?
!task.ext.container_tag ? "nfcore/vep:${task.ext.container_tag}" :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' : 'https://depot.galaxyproject.org/singularity/ensembl-vep:104.3--pl5262h4a94de4_0' :
'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' : 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }"
"nfcore/vep:${task.ext.container_tag}" }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

9
modules/snpeff/main.nf
View file

@ -1,12 +1,13 @@
process SNPEFF { process SNPEFF {
tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::snpeff=5.0" : null) conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ task.ext.container_tag ?
!task.ext.container_tag ? "nfcore/snpeff:${task.ext.container_tag}" :
workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' : 'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' : 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
"nfcore/snpeff:${task.ext.container_tag}" }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)