Feat/clade display names by rneher · Pull Request #1065 · nextstrain/ncov (original) (raw)
added 4 commits
- add clade renaming file names to parameter.yml
- fix renaming script
renaming if no clade mapping is defined.
Previously, clade colors were restricted to terms in the metadata. This is now changed to using the metadata which ensures that final clades (after modification through renaming to display clades) are used for color selection. We previously relied here on metadata, but display names are not present there.
- add missing 19A to name translation table
- rename clades file to match documentation
- canonicize clade name in emergence date table
corneliusroemer added a commit to neherlab/nextclade_data_workflows that referenced this pull request
See nextstrain/ncov#1065 Clade legacy is hence deprecated We now have a new column "display clade name" which is a combination of Nextstrain clade and Pango lineage, e.g. "23B (XBB.1.16)"
corneliusroemer added a commit to nextstrain/ncov-ingest that referenced this pull request
Starting with dataset release 2023-06-16 Nextclade no longer outputs a clades_legacy column into the tsv
( This was implemented in neherlab/nextclade_data_workflows#42
And triggered by a refactor in ncov of how we annotate clades nextstrain/ncov#1065 )
So as not to break downstream workflows that rely on ingest output metadata.tsv having clade_legacy, this PR adds a clade_legacy column to metadata.tsv
The values are defined as a simple mapping from clade_nextstrain (year-letter, e.g. 22F) to clade_legacy in defaults/clade-legacy-mapping.yml
This file lives in ingest for now to make this PR work without requiring changes to ncov.
corneliusroemer added a commit to nextstrain/ncov-ingest that referenced this pull request
Starting with dataset release 2023-06-16 Nextclade no longer outputs a clades_legacy column into the tsv
( This was implemented in neherlab/nextclade_data_workflows#42
And triggered by a refactor in ncov of how we annotate clades nextstrain/ncov#1065 )
So as not to break downstream workflows that rely on ingest output metadata.tsv having clade_legacy, this PR adds a clade_legacy column to metadata.tsv
The values are defined as a simple mapping from clade_nextstrain (year-letter, e.g. 22F) to clade_legacy in defaults/clade-legacy-mapping.yml
This file lives in ingest for now to make this PR work without requiring changes to ncov.
joverlee521 added a commit that referenced this pull request
The clade labels were updated in #1065.
Update the clade label so that the assign_rbd_levels script can find
the correct basal clade.
I had considered pulling this value out as a parameter in the config YAML, but the original commit message¹ implies that this shouldn't not be configurable.
¹ fb5f44e
joverlee521 added a commit that referenced this pull request
The clade labels were updated in #1065.
Update the clade label so that the assign_rbd_levels script can find
the correct basal clade.
I had considered pulling this value out as a parameter in the config YAML, but the original commit message¹ implies that this shouldn't not be configurable.
¹ fb5f44e
joverlee521 added a commit that referenced this pull request
The clade labels were updated in #1065.
Update the clade label so that the assign_rbd_levels script can find
the correct basal clade.
I had considered pulling this value out as a parameter in the config YAML, but the original commit message¹ implies that this should not be configurable.
¹ fb5f44e
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