port getGenomeAttribute() from TEMPLATE #26
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maxulysse
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nvnieuwk
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Oct 22, 2025
nvnieuwk
approved these changes
Oct 22, 2025
maxulysse
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Oct 22, 2025
maxulysse
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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
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That would help the migration to references and help clean TEMPLATE