Documentation about the PR reviewing process

[maxulysse]

Following a discussion with @sateeshperi we figured it would be a good idea to have some documentation/guidelines about how to actually do a review (I'm thinking also with some specifics about modules, pipelines, tools, website, release...)
It would be super helpful for newcomers.

[maxulysse]

@mahesh-panchal probably gave some good insight on this idea as well as usual :-D

[sateeshperi]

leaving points here...to be structured later...plz add as you see fit @maxulysse @mahesh-panchal @FriederikeHanssen

when all checks pass

• all optional params must go to $args
• must include tests for all output including optional
• optimize the software version extraction command if required
• check meta.yml for documentation links; patterns of files;
• check if the bioconda version of tool is latest ?

when tests fail

• linting fails
• conda fails
• docker fails

[mahesh-panchal]

• Run tool help and check important input ( usually optional ) has not been missed.
• Check module is suitable for offline running, e.g. from secure servers with no Internet.
  • No automatic database downloads assumed.
• Remove temporary unzipped files ( otherwise benefit is completely mitigated and problem made worse).
• Check all outputs are captured, by running the pytest (e.g. on Gitpod).

[mahesh-panchal]

• Check large outputs are compressed ( Do we have guidelines for gzip vs bzip2 vs something else?) - Add Compression tool guidance. Gzip vs bzip2 #1037

[FriederikeHanssen]

Good idea. Leaving this here: https://nf-co.re/developers/adding_modules#new-module-guidelines-and-pr-review-checklist

[mahesh-panchal]

Don't know where to put this so I'll just drop it here as a reminder, and may be helpful information for reviewing.
When running docker containers, Nextflow changes the --entrypoint to /bin/bash. Usually for some containers on Biocontainers (and others), the default entrypoint is /usr/local/env-execute, which then sets environment variables used by certain programs (e.g. Busco, Merqury). The files need to be sourced again to use them in container setting ( nf-core/modules#1239 (comment) )