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Checkm2 module #14

Merged
merged 13 commits into from
Oct 6, 2023
Merged

Checkm2 module #14

merged 13 commits into from
Oct 6, 2023

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KateSakharova
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@KateSakharova KateSakharova commented Sep 13, 2023 •
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I'm not able to add a proper test for checkm2 because it requires DB download.
Actions can't download DB because download script wants to change a json file

# OSError: [Errno 30] Read-only file system: '/usr/local/lib/python3.8/site-packages/checkm2/version/diamond_path.json'

That is why I added all tests with STUB command. They do check for empty directory and generate empty quality.tsv

mberacochea
mberacochea requested changes Sep 20, 2023
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Thank you @KateSakharova .. I've added some comments and suggestions

mberacochea
mberacochea approved these changes Sep 29, 2023
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:nice:... I think we can merge this... as discussed over slack :)

@KateSakharova
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test DB can't be available yet because of chklovski/CheckM2#81

@KateSakharova KateSakharova merged commit e2204d4 into main Oct 6, 2023
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@KateSakharova KateSakharova deleted the modules/checkm2 branch October 6, 2023 12:48
Ales-ibt pushed a commit that referenced this pull request Feb 14, 2024
@KateSakharova
Merge pull request #14 from EBI-Metagenomics/modules/checkm2
a716fe6 
Added Checkm2 module (tests only in stub mode)
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@chrisAta chrisAta chrisAta left review comments

@vagkaratzas vagkaratzas vagkaratzas left review comments

@mberacochea mberacochea mberacochea approved these changes

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@KateSakharova @mberacochea @vagkaratzas @chrisAta