CLI helper to select EDAM ontologies for module inputs / outputs

[ewels]

See nf-core/modules#5831 for background.

We should have a CLI auto-complete selection of EDAM ontologies for each module meta.yml input and output. Ability to select multiple.

Depends on #3026 as the bio.tools identifiers should form a shortlist / top ranked results or something. Exact UX for this needs some thought.

[ewels]

Instead of a CLI helper, let's start by simply syncing the EDAM ontologies from bio.tools to the meta.yml.

Folks can still manually edit this file if they wish, as any custom edits won't be clobbered.

We can revisit this at a later date if we feel that significant manual curation is still required, and reevaluate whether a CLI helpers is needed.

[ewels]

• Automate what we can, finish up the automation
• Add inline comments after each EDAM ontology term with a plain-text description of that term
  • Lint / auto-fix this.

[ewels]

nf-core/modules#7430

[mirpedrol]

#3418 EDAM ontologies are now added to the meta.yml file when a module is created. They are also added when possible during linting --fix. The bio.tools information is also used (if available) to generate the main.nf input and output channels when a module is created.

A CLI helper will be done on a separate PR.

[ewels]

Nearly there - hit an error when ontologies is not set as a key in the meta.yml file at all.

[ewels]

To write:

• Documentation
  • CLI tooling
  • Module specs for meta.yml
  • Tutorial
• Blog post?