nf-core / nf-core/tools

Issue with EDAM ontologies file extension

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#3,511 3 comments 0 reactions 1 assignee View on GitHub

@toniher is already working on this.

Since Mar 26, 2025.

bug
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Description

Description of the bug

I am checking EDAM ontologies automatic assignment loading process here:

https://github.com/nf-core/tools/blob/3ee0bea6de143092d98cacf063c0e435708c8813/nf_core/modules/modules_utils.py#L104

Now, extension is retrieved and processed from the second [1] column of EDAM.tsv. I would rather use an intended field for that, the 15th [14]. With the present assignment, there are some file extensions that are not used in real life (e.g., such as uniprotkb). As a drawback, there may be extensions appearing several times, e.g., json:

json,http://edamontology.org/format_3464
json,http://edamontology.org/format_3969
json,http://edamontology.org/format_3970

In these cases, I would favour assigning the most generic one, that I would hope is the first one is first created in the dictionary (so no overwriting would be allowed).
This will lead to less automatic assignation of filetypes, but more precise ones. Users would need to be recommended to curate manually when more specific EDAM mapping might exist for some specific file extensions such as JSON (e.g., http://edamontology.org/format_3970)

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