nf-core / nf-core/tools

CLI helper to select EDAM ontologies for module inputs / outputs

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#3,027 6 comments 0 reactions 1 assignee View on GitHub

@mirpedrol is already working on this.

Since Jan 16, 2025.

command line tools modules
Dominant language
Python
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Merged PRs (30d)
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Description

See https://github.com/nf-core/modules/issues/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 https://github.com/nf-core/tools/issues/3026 as the bio.tools identifiers should form a shortlist / top ranked results or something. Exact UX for this needs some thought.

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