Migrate to Nextclade v3 - Githubissues

nextstrain / pathogen-repo-guide

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Migrate to Nextclade v3 #69

Closed joverlee521 closed 2 weeks ago

joverlee521 commented 3 weeks ago

Migration to Nextclade v3 guide for reference.

Ingest workflow was migrated in https://github.com/nextstrain/pathogen-repo-guide/pull/54.

TODOs

[x] verify/update nextclade input files in nextclade/rules/export.smk
[x] update nextclade2 command in nextclade/build-configs/test-dataset/test_dataset.smk