Reviewing nf-core components

Component reviews ensure that modules and subworkflows meet nf-core standards before they reach the community. When you review a component pull request, you examine a new component submission or proposed changes to an existing component and provide constructive feedback before maintainers merge them into the nf-core repository.

The team of maintainers oversees the review process for components, but community input helps catch issues and ensures components work well across different use cases. Your perspective as a user of the components is valuable, particularly if you’ve used the tool before or understand common use cases.

General

Start by verifying that the component meets the general specifications:

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

You can cover most of the specifications by checking for the following:

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

Review the main module file

Check modules/nf-core/<module_name>/main.nf for:

• All optional parameters are in the $args section
• Software version extraction command is optimised, if required
• Bioconda version of the tool is the latest version
• Code removes temporary unzipped files to avoid mitigating benefits and worsening problems
• Large outputs use the correct compression tool (follow guidelines for gzip vs bzip2 vs other options)
  Tip

  Check the tool’s documentation or help text to ensure important optional parameters haven’t been missed. Run the tool help command if you’re unsure about available options.

Review tests and metadata

Check ../tests/modules/nf-core/<module_name>/main.nf and meta.yml for:

• Tests exist for all outputs, including optional ones
• meta.yml file has correct documentation links and patterns of files
• meta.yml file has correct bio.tools ID for the tool and correct EDAM ontology links of files
• Tool help has been checked to ensure important input (usually optional) has not been missed
• nf-test runs successfully (for example, on Gitpod) and captures all outputs