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Merged
merged 7 commits into from
Nov 13, 2025
Merged

Important! Template update for nf-core/tools v3.4.1 #1614

merged 7 commits into from
Nov 13, 2025

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@nf-core-bot nf-core-bot commented Oct 16, 2025 •
edited by pinin4fjords
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Version 3.4.1 of 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-3.4.1 branch (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 v3.4.1 release page.

✅ Merge Conflicts Resolved

All merge conflicts have been resolved following nf-core best practices and the patterns from nf-core/sarek#2031.

Resolution Strategy

Conflicts were resolved by keeping pipeline-specific features while adopting template infrastructure improvements:

Template Infrastructure Improvements (Adopted)

  • nf-test v0.9.3: Updated from v0.9.2 (removed custom diff settings as they're now defaults)
  • Nextflow v25.04.0: Updated minimum required version from v24.10.5
  • New help system: Added parameters for --help, --help_full, --show_hidden with improved formatting
  • Updated utility subworkflows: git_sha values updated to latest versions
  • GitHub Actions best practice: Use vars.AWS_S3_BUCKET instead of secrets for non-sensitive config

Template Issues Fixed

  • AWS anonymous client config: Removed aws.client.anonymous setting as it breaks full size tests (see Slack discussion)
  • Release announcements workflow: Fixed incorrect step id (get_topics → get_description) and missing closing parenthesis in jq command

Pipeline-Specific Features (Retained)

  • Aligner matrix testing: Kept star_salmon and star_rsem matrix in AWS full tests
  • Sentieon support: Retained authentication environment variables for Sentieon STAR
  • Reproducible tests: Kept commit-pinned test data URL (prevents breakage from test-datasets changes)
  • Test snapshot filtering: Kept removeFromYamlMap() to exclude entire Workflow section (both Nextflow and pipeline versions)
  • Pipeline metadata: Preserved real Zenodo DOI and complete pipeline description in ro-crate-metadata.json
  • CHANGELOG format: Maintained existing ## dev - xxxx-xx-xx convention

Merged Additions

  • Test ignore patterns: Combined both pipeline-specific (bbsplit, kallisto, star_rsem) and template patterns (multiqc, fastqc)

Files with Conflicts Resolved

10 files resolved (click to expand)
  1. .github/workflows/awsfulltest.yml - AWS testing configuration
  2. .github/workflows/nf-test.yml - nf-test workflow configuration
  3. CHANGELOG.md - Development version header
  4. main.nf - Pipeline initialization parameters
  5. modules.json - Module and subworkflow versions
  6. nextflow.config - Pipeline configuration and manifest
  7. ro-crate-metadata.json - Pipeline metadata
  8. subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf - Utility subworkflow
  9. tests/.nftignore - Test snapshot ignore patterns
  10. tests/default.nf.test - Test configuration

Additional Updates

  • Linting fixes: Applied rocrate_readme_sync fix to sync RO-Crate description with README.md
  • Test compatibility: Updated PIPELINE_INITIALISATION test to include new help parameters
  • Template bug fixes: Fixed release-announcements.yml workflow issues introduced in template

Testing Recommendations

  • Run nf-core lint to verify template compliance
  • Execute test profile to ensure all changes work correctly
  • Verify Sentieon-specific tests still function with authentication

References

🤖 Conflict resolutions by Claude Code

nf-core-bot and others added 2 commits October 16, 2025 13:39
@nf-core-bot
Template update for nf-core/tools version 3.4.1
2732654
@pinin4fjords @claude
Resolve nf-core template merge conflicts for v3.4.1
e826c0b 
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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github-actions bot commented Nov 13, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3df7533

+| ✅ 286 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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
  • 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 nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-13 11:56:36

FriederikeHanssen
FriederikeHanssen reviewed Nov 13, 2025
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jfy133
jfy133 reviewed Nov 13, 2025
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One minor fix for something that was borked in the template but otherwise LGTM

@pinin4fjords
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pinin4fjords commented Nov 13, 2025

Thanks @FriederikeHanssen @jfy133 !

@pinin4fjords pinin4fjords merged commit 680e989 into dev Nov 13, 2025
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pinin4fjords added a commit to pontushojer/nfcore-rnaseq that referenced this pull request Nov 13, 2025
@pinin4fjords @claude
Update CHANGELOG.md for PRs nf-core#1613 and nf-core#1614
45bded1 
- Add entry for PR nf-core#1613: Fix broken link and add latest kit version for Takara UMI prep
- Add entry for PR nf-core#1614: Template update for nf-core/tools v3.4.1

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords pinin4fjords added this to the 3.22.0 milestone Nov 14, 2025
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@pinin4fjords pinin4fjords pinin4fjords left review comments

@jfy133 jfy133 jfy133 left review comments

@mashehu mashehu mashehu approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

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