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BenKaehler / readytowear

Ready-made Taxonomic Weights Repository
BSD 3-Clause "New" or "Revised" License
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Add SILVA 138.1 weights #20

Closed nbokulich closed 2 years ago

nbokulich commented 2 years ago

We only have version 138 weights. 138.1 has been requested...

BenKaehler commented 2 years ago

Just linking this back to the original conversation.

antonija-kolobaric commented 2 years ago

Hello fellow microbiome enthusiasts! Following up on this and the OG conversation -- has anyone generated 138.1 weights? If yes, could they do a pull? If no, I can go ahead and try to do it

nbokulich commented 2 years ago

Hi @antonija-kolobaric , Thanks for checking in! At the moment this is blocked because we are waiting on pre-trained SILVA 138.1 classifiers to be released on the QIIME 2 data-resources page (so that the weights correspond to the classifiers released there). That in turn is blocked by this PR.

As we want the classifiers and weights to match, clawback is tied to the release cycle of the data-resources at the moment.

As a temporary solution we can duplicate the classifier training steps from here and the SILVA parts from here and port them over to here... at which point (to make most efficient use of resources) we should maybe also transition to a nextflow or snakemake workflow. Is this something that you would be interested in assisting with @antonija-kolobaric ?

antonija-kolobaric commented 2 years ago

Oh, ok I see where the issue is. I don't have a whole lot of experience with this, but I would be willing to give it a try, for sure!