Important! Template update for nf-core/tools v3.4.1 #2031
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nf-core-bot
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FriederikeHanssen and
maxulysse
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maxulysse
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Nov 11, 2025
maxulysse
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maxulysse
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Nov 12, 2025
maxulysse
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| testing* | ||
| *.pyc | ||
| bin/ | ||
| .nf-test/ |
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I don't think we need to have this path as it's in the .gitignore, and won't be commit ever
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Let's wait on #2054 to fix the failing tests |
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Merged dev branch into nf-core-template-merge-3.4.1, resolving conflicts by keeping pipeline-specific features while adopting template improvements. ## Conflict resolutions: ### Infrastructure improvements (adopted from template): - Update nf-test to v0.9.3 - Update minimum Nextflow version to 25.04.0 - Add new help system parameters (--help, --help_full, --show_hidden) - Update utility subworkflow git_sha values - Adopt `removeNextflowVersion` function for test snapshots - Use vars.AWS_S3_BUCKET instead of secrets for non-sensitive config ### Pipeline-specific features (retained): - Keep aligner matrix testing (star_salmon, star_rsem) in AWS full tests - Retain Sentieon authentication environment variables - Keep commit-pinned test data URL for reproducibility - Preserve pipeline metadata and real Zenodo DOI - Maintain existing CHANGELOG format ### Merged additions: - Combined test ignore patterns (both pipeline-specific and template) - Added both fastqc pattern variants for compatibility All changes follow the principle of preserving pipeline functionality while adopting template infrastructure improvements for better maintainability. Follows merge patterns from nf-core/sarek#2031 and guidance from https://nf-co.re/docs/tutorials/sync/merging_automated_prs 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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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: 3.4.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Closing in favor of #2058 |
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Version
3.4.1of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-3.4.1branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.
For more information about this release of nf-core/tools, please see the
v3.4.1release page.