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CLI helper to select EDAM ontologies for module inputs / outputs #3027

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ewels opened this issue Jun 19, 2024 · 1 comment
Open

CLI helper to select EDAM ontologies for module inputs / outputs #3027

ewels opened this issue Jun 19, 2024 · 1 comment
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command line tools Anything to do with the cli interfaces modules Related to tools for working with DSL2 modules

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@ewels
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ewels commented Jun 19, 2024

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 ewels added command line tools Anything to do with the cli interfaces modules Related to tools for working with DSL2 modules labels Jun 19, 2024
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ewels commented Jan 27, 2025

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.

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Labels
command line tools Anything to do with the cli interfaces modules Related to tools for working with DSL2 modules
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