Do: nf-core principles

• Does the pipeline meet the general nf-core guidelines?

Do: Local code and modules

• Do local scripts in bin/ have author and license embedded?
  • Local script licenses if written for the pipeline should not GPL, but ideally MIT (matching with pipeline code, upon which is assumed if not otherwise specified)
• Do all local modules have docker/singularity/conda declarations?
  • Are they ideally in bioconda/biocontainers
• Do all local modules conda/container tool declarations have versions? (and not latest, dev etc.)
• Do all local modules report versions (if applicable)?
  • Simple modules with e.g. single grep operations not necessary
  • It would be good to add with more complex operations such as awk
• Should any local modules be in nf-core/modules?

Do: Documentation

• Documentation is only on the nf-core website (not pointed to other non-nf-core standard places, e.g. not read the docs )
• Is documentation sufficiently described (usage.md, output.md, nextflow_schema.json)?
  • nextflow_schema.json: check if types are correct and that default and enum are used where applicable
• Are there any typos in the documentation (usage.md, output.md, nextflow_schema.json)
• Is CHANGELOG sufficiently filled in?
  • Check version system is three-point SemVer e.g. 2.1.0
  • Has the date been updated?
• Check citation formatting consistency in CIATIONS.md
• Check that all tools are cited
• Check that (all) pipeline author(s) listed themselves in the manifest and other contributors are added in the README

Do: Code

• Check no overly non-template components (no read the docs, entirely custom logo etc.)
• Check for general code readability
• Check for possible code bugs
• Check for consistency in parameters
  • i.e. snake_case
  • All boolean parameters evaluate to false (e.g. bad: params.run_step = true{:groovy}, good: params.skip_step = false{:groovy} )
• Check manifest includes DOI (if present) etc.

Don't have to do

• Review module code from nf-core/modules
• Comment on scientific content (unless you are familiar with the topic)
• Major code optimisation
  • You can suggest small code optimisations
  • Larger ones you can recommend, but shouldn't necessarily be require for release (hopefully this should have been covered during development PRs)