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Migrate local modules to nf-core containers format - #311

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module-standardization
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Migrate local modules to nf-core containers format#311
nictru wants to merge 3 commits into
devfrom
module-standardization

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@nictru nictru commented Aug 10, 2026

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Migrate local modules to nf-core containers format.
4dbdcbb 
Add meta.yml documentation, Wave container URIs, and conda lock files for
local modules via nf-core modules containers create, and regenerate
conf/containers_*.config. GPU modules (scvitools, scimilarity) and
scarches/expimap are excluded where Wave builds failed or GPU containers
are required.

Generated by Composer
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github-actions Bot commented Aug 10, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

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github-actions Bot commented Aug 10, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3f98837

+| ✅ 318 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  15 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-08-10 19:21:26

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github-actions Bot commented Aug 10, 2026 •
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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 12/25

See the full run for details.

nictru added 2 commits August 10, 2026 21:18
@nictru
Update nf-test snapshots for migrated local module containers.
21c4198 
Regenerate snapshots for 27 local modules after Wave container migration
via nftu. Modules with failing process tests are excluded.

Generated by Composer
@nictru
Update remaining nf-test snapshots for migrated local modules.
3f98837 
Regenerate snapshots for 25 additional local modules after Wave container
migration via nftu.

Generated by Composer
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