Review checklist for pipeline releases

When you review a PR, you examine a pipeline release submission. You provide constructive feedback on those changes before the maintainers merge them into the nf-core repository. Your review ensures that the pipeline meets the coding standards of the project, maintains consistency and achieves high quality.

Use this guide to evaluate nf-core pipeline release pull requests. Focus on checking for adherence to nf-core principles rather than applying strict universal criteria, given the diverse nature of pipeline releases.

Do: nf-core principles

• Verify that the pipeline meets the general nf-core guidelines.

Do: Local code and modules

• Check that local scripts in bin/ include author and licence information.
• Check that licences are MIT (not GPL) to match pipeline code.
• Ensure all local modules have docker/singularity/conda declarations, preferably from bioconda/biocontainers.
• Verify the code specifies tool versions (avoiding latest or dev tags).
• Check that complex modules include version reporting.
• Evaluate whether local modules belong in nf-core/modules instead.

Do: Documentation

• Verify documentation appears only on the nf-core website.
• Check that usage.md, output.md, and nextflow_schema.json are comprehensive.
• Check schema for correct types, appropriate use of default and enum fields.
• Proofread documentation for errors.
• Ensure CHANGELOG follows three-point semantic versioning (for example, 2.1.0) with updated dates.
• Verify consistent citation formatting in CITATIONS.md.
• Confirm the documentation properly credits all tools and authors.

Do: Code

• Assess general readability and potential bugs.
• Ensure parameter consistency using snake_case.
• Verify boolean parameters default to false (prefer skip_step = false over run_step = true).
• Check manifest includes DOI when applicable.

Don’t have to do

• Review code from nf-core/modules.
• Comment on scientific accuracy unless qualified.
• Demand major code optimisation (minor suggestions acceptable).