From 69e7fb7312a20c746e6752736aa5a684e6174009 Mon Sep 17 00:00:00 2001 From: LysianeBouchard Date: Tue, 17 Dec 2024 19:27:38 -0500 Subject: [PATCH] fix: CLIN-3610 use container tag 1.20 instead latest for split multiallelics --- CHANGELOG.md | 3 +++ conf/modules.config | 1 + modules/local/split_multi_allelics.nf | 4 +--- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2fcdcc2..6d67a30 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#49](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/49) Add support for local frequency source - [#49](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/49) Pass java -Xmx option at the command line for exomiser +### `Fixed` +- [#50](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/50) Use container tag 1.20 for splitMultiAllelics process + ### `Known issues` - The nf-core modules that we are using have a potential performance flaw. Typically, the regex used to describe the output files also match the input files (ex: "*.vcf"), which can cause unnecessary file transfers. This has already proven to cause issues on fusion. One fix could be to transfer the whole modules to local to perform the small change necessary to fix this. - The VEP cache version used in the CQDG environment (112) does not match the default configured VEP version (111). This issue can be avoided by overriding the Docker container of the ensemblevep process. If no project is using VEP version 111, it should not be used as the default value. diff --git a/conf/modules.config b/conf/modules.config index 9abcf0b..0e9cea6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -95,6 +95,7 @@ process { } withName: 'splitMultiAllelics' { + container = 'staphb/bcftools:1.20' publishDir = new_publish_dir([enabled: true]) } } diff --git a/modules/local/split_multi_allelics.nf b/modules/local/split_multi_allelics.nf index 850bdc0..6534cdf 100644 --- a/modules/local/split_multi_allelics.nf +++ b/modules/local/split_multi_allelics.nf @@ -1,9 +1,7 @@ // This module does not follow nf-core standards. We plan to fix or replace it with an nf-core module in the future. process splitMultiAllelics{ - label 'medium' + label 'process_medium' - container 'staphb/bcftools' - input: tuple val(meta), path(vcfFile) path referenceGenome