[Migration to Nextclade v3 guide](https://docs.nextstrain.org/projects/nextclade/en/stable/user/migration-v3.html) for reference. ## TODOs - [x] remove `use_nextalign` config from build.yaml files (the use of the config was removed in https://github.com/nextstrain/ncov/pull/630) - [x] ~update [mutation_summary.py](https://github.com/nextstrain/ncov/blob/7e594bc85ac82c4d499555f5288ffd6628dbd141/scripts/mutation_summary.py) to work with Nextclade v3 outputs~ Remove mutation_summary.py and related rules - [x] update nextclade2/nextalign commands in workflow rules - [x] remove references to "nextalign" in docs - [x] update nextclade dependencies [workflow/envs/nextstrain.yaml](https://github.com/nextstrain/ncov/blob/7e594bc85ac82c4d499555f5288ffd6628dbd141/workflow/envs/nextstrain.yaml#L10-L11) - [x] major release of the workflow
Migration to Nextclade v3 guide for reference.
TODOs
use_nextalignconfig from build.yaml files (the use of the config was removed in Include distances and explicit aa muts by default #630)update mutation_summary.py to work with Nextclade v3 outputsRemove mutation_summary.py and related rules