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Add a map of Nextstrain clade to Pango lineage #1159

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huddlej
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@huddlej huddlej commented Oct 23, 2024

Description of proposed changes

Adds an official map between Nextstrain clade and Nextclade pango lineage to support analyses that need to convert between these two lineage naming systems.

Inspired by discussion in the variant nowcasting hub.

This may warrant a new release as a way to let people know we've provided this file.

This PR may also require some additional documentation whereever the clade update process is documented.

Related issue(s)

Related to #1152, etc.

Testing

What steps should be taken to test the changes you've proposed?
If you added or changed behavior in the codebase, did you update the tests, or do you need help with this?

Release checklist

If this pull request introduces backward incompatible changes, complete the following steps for a new release of the workflow:

  • Determine the version number for the new release by incrementing the most recent release (e.g., "v2" from "v1").
  • Update docs/src/reference/change_log.md in this pull request to document these changes and the new version number.
  • After merging, create a new GitHub release with the new version number as the tag and release title.

If this pull request introduces new features, complete the following steps:

  • Update docs/src/reference/change_log.md in this pull request to document these changes by the date they were added.

Adds an official map between Nextstrain clade and Nextclade pango
lineage to support analyses that need to convert between these two
lineage naming systems.
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@joverlee521 joverlee521 left a comment

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I'm surprised this doesn't already exist! The closest I could find is the defaults/clade_display_names.yml file.

I am slightly worried that this might get out of sync or forgotten because it's not actively used in the workflow...

@victorlin
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+1 for additional documentation to keep this up to date

@huddlej
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huddlej commented Oct 30, 2024

Thank you, @victorlin and @joverlee521! I actually created the file in this PR by parsing that clade display names YAML! 😄

It turns out the original poster in the nowcasting hub discussion wanted a way to switch from Pango lineage to Nextstrain clade which this PR doesn't address.

As I described in the related Slack thread, it's more of a pain to get from Nextstrain clade to Pango lineage, but since no one is asking for that right now maybe we don't need this additional complexity.

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3 participants