Migrate to Nextclade v3

nextstrain / mpox

Nextstrain build for mpox virus

https://nextstrain.org/mpox

MIT License

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Migrate to Nextclade v3 #280

Open joverlee521 opened 1 week ago

joverlee521 commented 1 week ago

Migration to Nextclade v3 guide for reference.

Phylogenetic workflow was migrated in https://github.com/nextstrain/mpox/pull/245.

TODOs

[x] update nextclade2 commands in ingest rules
[x] update files uploaded to S3 in ingest/nextstrain_automation
[x] Remove reference to nextalign in phylogenetic/defaults/description.md
[x] Update files linked in phylogenetic/defaults/description.md

joverlee521 commented 1 week ago

Tracked down why we are currently using both MPXV and hMPXV Nextclade datasets in https://github.com/nextstrain/mpox/pull/114#discussion_r958185115:

align now uses hmpxv. shouldn't matter much in practice, but I think people will be more confidence when the alignment is based on an actual sequence, rather than a reconstructed ancestor.

Since the v3 Nextclade datasets for MPXV and hMPXV both use NC_063383.1 as the reference, we can just run Nextclade once using the MPXV dataset.