release-prep

为 nf-core 流水线做好发布准备。在发布新版本之前、检查发布就绪情况、完成发布清单，或最终完善发布相关文档时，可使用此技能。

SKILL.md

--- frontmatter

name: release-prep
description: Prepare an nf-core pipeline for release. Use before releasing a new version, when checking release readiness, completing the release checklist, or finalizing documentation for a release.
argument-hint: "[version]"
disable-model-invocation: true
allowed-tools:
  - Bash(conda run -n nf-core *)
  - Read
  - Edit
  - Write
  - Glob
  - Grep

nf-core Pipeline Release Preparation

Comprehensive checklist and process for preparing an nf-core pipeline release.

Quick Commands

bash

# Run full lint suite
conda run -n nf-core nf-core pipelines lint

# Run all tests
conda run -n nf-core nf-test test

# Check versions
grep -r "version" nextflow.config | head -20

# Validate schema
conda run -n nf-core nf-core pipelines schema lint

Release Checklist

1. Version Number

• Update manifest.version in nextflow.config
• Follow semantic versioning: MAJOR.MINOR.PATCH
• Version matches across all files

nextflow

// nextflow.config
manifest {
    version = '2.1.0'
}

2. CHANGELOG.md

• Add new version section with date
• List all changes since last release
• Categorize: Added, Changed, Fixed, Deprecated, Removed
• Credit contributors

markdown

## [2.1.0] - 2024-01-15

### Added
- New feature X (#123)

### Changed
- Updated module Y to v2.0 (#124)

### Fixed
- Bug in process Z (#125)

### Contributors
@contributor1, @contributor2

3. Documentation

• docs/usage.md - Accurate usage instructions
• docs/output.md - All outputs documented
• README.md - Up to date
• nextflow_schema.json - All params documented

4. Code Quality

• All lint tests pass: nf-core pipelines lint
• All nf-tests pass: nf-test test
• CI/CD tests pass on GitHub
• No TODO comments in code
• Code is readable and maintainable

5. Parameters

• All use snake_case naming
• Boolean params use negative naming (skip_X not run_X)
• Defaults are sensible
• Required params clearly marked
• Schema validates correctly

6. Modules & Subworkflows

• All modules updated to latest versions
• Local modules properly documented
• Module tests pass

7. Containers

• All tools have versioned containers
• No :latest tags
• Both Docker and Singularity work

8. Citations

• CITATIONS.md lists all tools
• Proper citation format
• DOIs where available

9. Final Checks

• Test profile works: nextflow run . -profile test,docker
• Full test passes: nextflow run . -profile test_full,docker
• AWS tests pass (if applicable)

Pre-Release Process

Step 1: Update Dev Branch

bash

git checkout dev
git pull origin dev

Step 2: Run Full Lint

bash

conda run -n nf-core nf-core pipelines lint
# Fix any issues

Step 3: Run All Tests

bash

conda run -n nf-core nf-test test --profile docker
# Ensure all pass

Step 4: Update Version

bash

# Edit nextflow.config
# manifest.version = 'X.Y.Z'

Step 5: Update CHANGELOG

bash

# Add version section with date
# List all changes

Step 6: Final Commit to Dev

bash

git add -A
git commit -m "Prepare release X.Y.Z"
git push origin dev

Step 7: Create Release PR

bash

# Create PR from dev to master
gh pr create --base master --head dev --title "Release X.Y.Z"

Step 8: Review & Merge

•Wait for CI tests
•Get two approvals
•Merge to master

Step 9: Create GitHub Release

bash

# Tag the release
git checkout master
git pull
git tag -a X.Y.Z -m "Release X.Y.Z"
git push origin X.Y.Z

# Create release on GitHub with notes from CHANGELOG

Version Numbering Guide

Change Type	Version Bump	Example
Breaking changes	MAJOR	1.0.0 → 2.0.0
New features	MINOR	1.0.0 → 1.1.0
Bug fixes	PATCH	1.0.0 → 1.0.1

Common Release Issues

Lint Failures

bash

# Run with fix flag
conda run -n nf-core nf-core pipelines lint --fix

Version Mismatch

Check these files match:

•nextflow.config (manifest.version)
•CHANGELOG.md (latest version)

Missing Citations

bash

# Find tools without citations
grep -r "process " modules/ | grep -v "CITATIONS"

Schema Out of Sync

bash

# Rebuild schema
conda run -n nf-core nf-core pipelines schema build

Post-Release

•Announce: Post on nf-core Slack
•DOI: Register new version on Zenodo
•Update docs: Refresh website documentation
•Merge back: Sync master changes to dev

bash

git checkout dev
git merge master
git push origin dev