From 6510a7ff4f339625ebb89055bd39b9063797bb63 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Tue, 7 Dec 2021 10:30:35 +0100 Subject: [PATCH] feat: add meta.id tag (#1116) * feat: add meat.id tag * fix: actually call the right container for singularity --- modules/ensemblvep/main.nf | 9 +++++---- modules/snpeff/main.nf | 9 +++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf index 9caffb0c..78f2712c 100644 --- a/modules/ensemblvep/main.nf +++ b/modules/ensemblvep/main.nf @@ -1,12 +1,13 @@ process ENSEMBLVEP { + tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::ensembl-vep=104.3" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - !task.ext.container_tag ? + 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' : - "nfcore/vep:${task.ext.container_tag}" }" + 'quay.io/biocontainers/ensembl-vep:104.3--pl5262h4a94de4_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf index db9cca72..9847c513 100644 --- a/modules/snpeff/main.nf +++ b/modules/snpeff/main.nf @@ -1,12 +1,13 @@ process SNPEFF { + tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::snpeff=5.0" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - !task.ext.container_tag ? + container "${ task.ext.container_tag ? + "nfcore/snpeff:${task.ext.container_tag}" : + workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' : - 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' : - "nfcore/snpeff:${task.ext.container_tag}" }" + 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }" input: tuple val(meta), path(vcf)