Contributing

Contributing

Contributions should keep the project portable, reproducible, and maintainable.

Before changing code

• Build the project with ./mvnw clean package.
• Understand whether the change affects GUI, CLI, pipeline, reports, runtime layout, or packaging.
• Keep GUI and CLI behavior consistent where possible.

Documentation expectations

When adding or changing features, update the relevant documentation:

• README only for project overview or quick-start changes
• Wiki pages for detailed user/developer documentation
• SVG diagrams if workflow, architecture, or release behavior changes
• screenshots when UI behavior changes

Runtime assets

Do not commit generated release output, Maven output, IDE folders, JavaFX SDK folders, or JDK/JRE folders.

Curated BBMap and BLAST+ runtime assets are intentionally part of the repository layout.

Recommended checks

./mvnw clean package
scripts/dev/verify-runtime-layout.sh

Pull request focus

Prefer focused changes that are easy to review.

For large refactors, explain:

• why the change is needed
• what behavior should remain unchanged
• what files or packages were moved
• what testing was performed