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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Update nextclade to latest >= 2.7.0 #68

Closed pbiology closed 1 year ago

pbiology commented 1 year ago

What needs to be done: Update the pipeline to include latest version of nextclade. The containers then needs to be built.

One probably needs to verify that this does not break any outputs

Suggestions on how to get it done:

What are the arguments for getting it done:

The version now is quite outdated and using it in production is quite questionable

Task is considered finished when: gms-artic outputs the nextclade files with an nextclade version >= 2.7.0

pbiology commented 1 year ago

I just assigned you now @JD2112 and @sofstam. You know better if someone else is better suited