Contributing

Tip

Keep process names stable in main.nf so documentation DAGs remain accurate.

Development rules

1. Do not change biological logic in Perl scripts without dedicated review.
2. Keep nextflow_schema.json synchronized with nextflow.config params.
3. Validate docs and pipeline changes together.

Local checks

Install the docs dependencies first:

pip install -r docs/requirements.txt

Then validate the pipeline and docs:

nextflow run main.nf -profile test
mkdocs build