Download clade definitions from GitHub #154
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Remove local copies of clade and subclade definitions for H1N1pdm, H3N2, and Vic and add configuration and rules to download these files from the corresponding GitHub repositories as needed by each workflow. This approach allows us to maintain local copies of clades and subclades for Yam and other exceptions to the standard maintained clades. Since we only need to maintain the two "clade systems" of "clade" and "subclade" for the main phylogenetic workflow, this commit defines a top-level mapping of clade file URLs to lineages and segments. This is in contrast to the build-specific clade mappings used by the Nextclade workflow [1]. [1] https://github.com/nextstrain/seasonal-flu/blob/d439f897f2819961dee431f92ea4e6f45343688a/nextclade/config/config_dict.yaml#L8-L16
rneher
approved these changes
Feb 23, 2024
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Description of proposed changes
Remove local copies of clade and subclade definitions for H1N1pdm, H3N2, and Vic and add configuration and rules to download these files from the corresponding GitHub repositories as needed by each workflow. This approach allows us to maintain local copies of clades and subclades for Yam and other exceptions to the standard maintained clades. Since we only need to maintain the two "clade systems" of "clade" and "subclade" for the main phylogenetic workflow, this commit defines a top-level mapping of clade file URLs to lineages and segments. This is in contrast to the build-specific clade mappings used by the Nextclade workflow (for example).
Note that we eventually want to assign clade labels with Nextclade instead of augur clades, so this implementation should get deleted when that change happens.
Checklist