pipeline start/complete messages are now at TRACE level #27
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
maxulysse
added a commit
that referenced
this pull request
Oct 29, 2025
* add getGenomeAttribute() and improve softwareVersionsToYAML() * pre-commit * use java 17 * fix tests * update CHANGELOG * downgrade pipeline starting / oncomplete to trace * split to #26 * Update CHANGELOG.md * Update CHANGELOG.md * split to #27 * forgot code * add docs and tests * remove workflow.trace * include review comments * fix suggestions * pre-commit * Code quality improvements for PR #24 (#30) * docs: fix typo in softwareVersionsToYAML documentation Fix typo in JavaDoc example code where 'versions_yamllet'' was incorrectly written instead of 'versions_yaml'. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> * refactor: simplify softwareVersionsToYAML with focused helper methods Refactored the complex 166-line softwareVersionsToYAML() method by extracting only essential helper methods that provide real value: Core improvements: - Main method now ~100 lines with visible, straightforward logic - Extracted 4 focused helper methods (down from original over-engineered 13): * processYamlContent(): Eliminates duplicate YAML parsing (used 5+ times) * mergeParsedYaml(): Handles complex nested/flat YAML detection logic * mergeProcessMap(): Reusable process map merging with key cleaning * hasToFileMethod(): Safety-critical reflection for Path detection - Type routing, simple string operations, and sorting kept inline - Uses small recursive closure for nested list handling - Eliminates deeply nested closures from original implementation Benefits: - Better balance between simplicity and maintainability - Main logic flow visible and easy to follow - Real complexity extracted to testable helpers - No thin wrapper methods adding unnecessary indirection - All tests pass without modification This approach keeps both Nextflow usage AND the code simple while improving on the original deeply-nested 166-line implementation. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> --------- Co-authored-by: Claude <[email protected]> --------- Co-authored-by: Edmund Miller <[email protected]> Co-authored-by: Claude <[email protected]>
edmundmiller
approved these changes
Oct 30, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changed pipeline start/complete messages from
logtoTRACElevel to reduce console noise in normal operationMainly for nf-core download