From 5851a1d1b0e675366def8dc5cb23e3181a536d4a Mon Sep 17 00:00:00 2001 From: Greg Date: Fri, 16 Aug 2024 11:29:25 -0700 Subject: [PATCH 1/2] replaced old MultiQC containers with nf-core/ubuntu:20.04 --- modules/local/adjust_maxbin2_ext.nf | 7 +++---- modules/local/rename_postdastool.nf | 7 +++---- modules/local/rename_predastool.nf | 7 +++---- 3 files changed, 9 insertions(+), 12 deletions(-) diff --git a/modules/local/adjust_maxbin2_ext.nf b/modules/local/adjust_maxbin2_ext.nf index 4d7fecd0..70eae99c 100644 --- a/modules/local/adjust_maxbin2_ext.nf +++ b/modules/local/adjust_maxbin2_ext.nf @@ -2,11 +2,10 @@ process ADJUST_MAXBIN2_EXT { tag "${meta.assembler}-${meta.id}" label 'process_low' - // Using container from multiqc since it'll be included anyway - conda "bioconda::multiqc=1.12" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'biocontainers/multiqc:1.12--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(bins) diff --git a/modules/local/rename_postdastool.nf b/modules/local/rename_postdastool.nf index 7d5a325e..6129dfbe 100644 --- a/modules/local/rename_postdastool.nf +++ b/modules/local/rename_postdastool.nf @@ -2,11 +2,10 @@ process RENAME_POSTDASTOOL { tag "${meta.assembler}-${meta.id}" label 'process_low' - // Using container from multiqc since it'll be included anyway - conda "bioconda::multiqc=1.12" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'biocontainers/multiqc:1.12--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(bins) diff --git a/modules/local/rename_predastool.nf b/modules/local/rename_predastool.nf index cc3bab18..3d9373b8 100644 --- a/modules/local/rename_predastool.nf +++ b/modules/local/rename_predastool.nf @@ -2,11 +2,10 @@ process RENAME_PREDASTOOL { tag "${meta.assembler}-${meta.binner}-${meta.id}" label 'process_low' - // Using container from multiqc since it'll be included anyway - conda "bioconda::multiqc=1.12" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'biocontainers/multiqc:1.12--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(bins) From bd0ef3b44a18fca004314563de7edc15de6b71a1 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 20 Aug 2024 08:35:22 +0200 Subject: [PATCH 2/2] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a260063b..129da60e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#648](https://github.com/nf-core/mag/pull/648) - Fix sample ID/assembly ID check failure when no IDs match (reported by @zackhenny, fix by @prototaxites) - [#646](https://github.com/nf-core/mag/pull/646) - GTDB-Tk directory input now creates a value channel so it runs for all entries to the process and not just the first (reported by @amizeranschi, fix by @prototaxites). - [#639](https://github.com/nf-core/mag/pull/639) - Fix pipeline failure when a sample produces only a single bin (fix by @d-callan) +- [#652](https://github.com/nf-core/mag/pull/651) - Replace base container for bash only modules to reduce number of containers in pipeline (reported and fixed by @harper357) ### `Dependencies`