Reviewing nf-core configs

nf-core/configs reviews ensure that configs adhere to the nf-core/config specifications and ensure consistency across all configs. When you review a nf-core/configs pull request, you examine a new config submission or proposed changes to an existing component and provide constructive feedback before maintainers merge them into the nf-core repository.

General

• Permission by infrastructure administrators confirmed

For institutional configs:

• Each config has a *.config Nextflow configuration file under conf/
• Each file has a *md documentation file under docs/
• Does not include withName or withLabel specifications
• Includes resourceLimits scope

For pipeline-specific institutional configs

• Each config targets a single pipeline
• Each config has a *.config Nextflow configuration file under conf/pipeline/<pipeline_name>/
• Each file has a *md documentation file under docs/pipeline/<pipeline_name>/

Naming

• The name is all lowercase
• The name includes only letters, numbers and/or underscores
• The name uses no other characters or punctuation
• If multiple clusters, uses an institutional suffix (e.g. ucl_ for all University College London [UCL] configs)

Config contents

• Each config adheres to the Nextflow strict syntax, for example with no warnings or errors from nextflow lint
• Each config includes parameters:
  • config_profile_description
  • config_profile_contact
  • config_profile_url
• Custom parameters:
  • Are documented
  • Are added to the ignoreParams option of the validation scope

For sensitive data or offline clusters (if applicable):

• Local container registry configured
• External downloads disabled or documented
• Data governance/policy requirements documented

Documentation

• Contains information on how to use the config in the context of the instruction
• (Optional) documentation includes additional recommendations (e.g., scratch, temporary, or environmental variables)
• Required parameter or environmental variables described
• All commands are copy-paste-able examples

Config infrastructure

• Entry added to nfcore_custom.config
• Entry added to .github/workflows/main.yaml