8000 Add support to supplying local copy of Krona taxonomy database · Issue #404 · nf-core/mag · GitHub
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Add support to supplying local copy of Krona taxonomy database #404

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jfy133 opened this issue Mar 10, 2023 · 0 comments
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Add support to supplying local copy of Krona taxonomy database #404

jfy133 opened this issue Mar 10, 2023 · 0 comments
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enhancement New feature or request

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jfy133 commented Mar 10, 2023

Description of feature

Currently either you skip Krona entirely, or you're forced to run a Krona download step when using containers.

The latter causes the pipeline to fail on no-internet-on-compute-node clusters.

We should give the option to supply a pre-downloaded krona taxonomy/database and supply this e.g. like --checkm_db and --cat_db etc.
@jfy133 jfy133 added the enhancement New feature or request label Mar 10, 2023
@jfy133 jfy133 mentioned this issue Aug 31, 2023
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jfy133 added a commit that referenced this issue Sep 2, 2023
@jfy133
Merge pull request #497 from willros/local-krona-db
21c9716 
Adds --krona_db parameter to point at a local copy of the db needed for Krona. Suggested in Issue #404.
@jfy133 jfy133 closed this as completed Sep 2, 2023
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