Review checklist for nf-core components

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

While the team of maintainers oversees the PR review process for components, these guidelines help you review PRs consistently and effectively as a community member. The following collection of community suggestions can guide your review process.

General

• All components adhere to the nf-core module specifications or subworkflow specifications.
• Ensure all checks pass, including linting, conda, singularity, and docker.

Otherwise, you can cover most of the specifications by checking for the following:

• Check that the component runs offline without assuming automatic database downloads.
• Check that Nextflow changes the --entrypoint to /bin/bash and that environment variables are sourced again when running docker containers.
• Check that it adheres to nf-core coding standards (for example, use of meta map).
• Check that the code is readable and the formatting is correct (for example, indenting, extra spaces).

modules/nf-core/modulename/main.nf

• Check that all optional parameters are in the $args section.
• Check that the software version extraction command is optimised, if required.
• Check if the bioconda version of the tool is the latest version.
• Ensure the code removes temporary unzipped files to avoid mitigating benefits and worsening problems.
• Ensure large outputs use the correct compression tool (follow guidelines for gzip vs bzip2 vs other options).

../tests/modules/nf-core/modulename/main.nf and meta.yml

• Check that there are tests for all outputs, including optional ones.
• Check that the meta.yml file has correct documentation links and patterns of files.
• Check that the meta.yml file has correct bio.tools ID for the tool and correct EDAM ontology links of files.
• Run the tool help and check that important input (usually optional) has not been missed.
• Run nf-test (for example, on Gitpod) to check that it captures all outputs.