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Update artic to version 1.6.1 #101

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DarianHole wants to merge 3 commits into master from update/artic

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DarianHole commented Feb 7, 2025

Updating the artic version to utilize the new features and variant calling with clair3

This DOES require parameter adjustments that are breaking so the version is going to 3.0.0.

Some parts to finish:

Parameter addition to optional --model
- See if its a string or path to determine with artic parameter is used, --model <str> or --model-dir <path>
- If no model given it'll detect best which is ok but needs code for it
Docs updates
- Removal of medaka mentions
- Removal of nanopolish mentions
- Addition of artic validation quick report
  - Link to artic if needed
Test updates

DarianHole added 3 commits

February 7, 2025 11:50


          env update for nextclade, artic, removal of defaults

31eb15c


          update artic and supporting files

0e59c23


          adjust ncov-tools environment

62ea4cf

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