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Post release version bump
Switch-to-self-hosted-runners
Json schema improvements
Fix fARGene config param
Add CODEOWNERs file for active maintainers
Important! Template update for nf-core/tools v3.2.1
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maxulysse
reviewed
Sep 18, 2025
maxulysse
reviewed
Sep 18, 2025
maxulysse
approved these changes
Sep 18, 2025
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Looks good to me.
Only minor things that could be improved on the testing side, but I know how long it can take, so no issue from me there
jfy133
approved these changes
Sep 18, 2025
| }, | ||
| "AMRFINDERPLUS_RUN": { | ||
| "amrfinderplus": "3.12.8", | ||
| "amrfinderplus-database": null |
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Minor thing for the future,, we should fix that
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That AI review request was a mistake, please disregard |
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Pull Request Overview
This release PR for v3.0.0 "French Chocolatine" updates the nf-core/funcscan pipeline with significant infrastructure and dependency changes. The PR includes updates to the nf-core template (3.2.1 → 3.3.2), upgrades antiSMASH (7.1.0 → 8.0.1) and RGI (6.0.3 → 6.0.5), and removes the deprecated --bgc_antismash_installdir parameter.
- Updated to nf-core template 3.3.2 with modernized CI/CD workflows
- Upgraded antiSMASH to v8.0.1 and RGI to v6.0.5 for improved functionality
- Fixed ABRicate sample ID handling and fARGene configuration issues
Reviewed Changes
Copilot reviewed 113 out of 120 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/*.nf.test | Updated test files with new profile declarations and fixed log file paths |
| modules/nf-core/antismash/* | Replaced antismashlite modules with full antismash implementation |
| modules/nf-core/rgi/* | Updated RGI modules to version 6.0.5 |
| modules/nf-core/abricate/run/* | Fixed sample ID handling in ABRicate output |
| .github/workflows/* | Modernized CI/CD with nf-test framework replacing older CI approach |
| conf/*.config | Added antismash database parameters and updated resource limits |
| nextflow.config | Updated version to 3.0.0 and removed deprecated parameters |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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The error: |
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Finally 🎉 was a space issue! |
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I'm just going to update AMRFinderplus & hAMRonization accordingly, and then we are good to go :) |
jfy133
reviewed
Oct 4, 2025
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v3.0.0 - French Chocolatine
AddedFixedext.args. (by @jasmezz)DependenciesDeprecated--bgc_antismash_installdiras new antiSMASH module container no longer requires mounting of this directory for execution. (by @mberacochea and @jfy133)PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).