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nf-core / funcscan

(Meta-)genome screening for functional and natural product gene sequences
https://nf-co.re/funcscan
MIT License
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DRAMP download error #423

Open jasmezz opened 2 weeks ago

jasmezz commented 2 weeks ago

Description of the bug

The DRAMP database issue reported by J.C. Ruitenberg (https://nfcore.slack.com/archives/C02K5GX2W93/p1728552583863299) seems to affect the DRAMP download and processing permanently since it was updated on September 8 (see: http://dramp.cpu-bioinfor.org/static/update.php) – 3 days after funcscan 2.0.0 release.

I reported the problem already to the DRAMP maintainers; if this is not going to be solved soon, the DRAMP download script bin/ampcombi_download.py should be updated on our side to not crash if non-ascii-characters are found in the database sheet during parsing.

Example error here: https://github.com/nf-core/funcscan/actions/runs/11293369456/job/31411353829?pr=422

Command used and terminal output

No response

Relevant files

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System information

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jasmezz commented 3 days ago

Still no reply from DRAMP maintainers (neither to my e-mail nor via uploading a fixed DRAMP database). I think we should go ahead and adapt the DRAMP download script, @Darcy220606 👾 If you check their homepage, they have it under CC-BY license. Meaning we could upload it on our side (Zenodo?) to track versions and provide a working DRAMP version. Either: