Add proposed subclades to public and private builds #195
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Updates build configs, Auspice configs, and workflow rules and scripts to surface proposed subclades in all public and private builds for all three lineages and both HA and NA.
Updates workflow rules and scripts to use proposed subclades from Nextclade annotations instead of the standard subclades. These changes affect monthly reporting and not the public builds.
1 task
Use subclade as default branch label in private builds, since Augur's validation of the Auspice config JSON doesn't allow default branch labels to have spaces, underscores, or hyphens [1]. [1] nextstrain/augur#1661
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Description of proposed changes
Updates the workflow configs, scripts, and rules to use proposed subclades instead of subclades in private builds and adds proposed subclades to public builds for all three lineages and both HA and NA.
As part of this update, I've also updated the color scales for subclades to reflect the variants circulating in the last 6 months with two or more sequences in the most recent public 2y builds.
Related issue(s)
Replaces #193
Follows from #194
Related to nextstrain/augur#1661
Checklist