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- add clade renaming file names to parameter.yml - fix renaming script
renaming if no clade mapping is defined.
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Trial runs should appear here: https://nextstrain.org/staging/ncov/open/trial/clade-display-names/global/all-time |
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this worked as expected. other than for the problem that the colors aren't generated properly since the display names are not in the metadata. |
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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.
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this now works happily: |
| @@ -0,0 +1,32 @@ | |||
| 19B: 19B | |||
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Is there a reason there's no 19A: 19A?
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none that I can think of ;)
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Once this is merged I'll have to adjust the Nextclade data workflows, so I'll see what you come up with here. If we wanted to maintain WHO names for colouring, would it make sense to define a I remember we talked about moving the ground truth to a separate "clade definition" repo - but we can also just have it in here, there's no real circularity. |
| lat_longs: "defaults/lat_longs.tsv" | ||
| description: "defaults/description.md" | ||
| clades: "defaults/clades.tsv" | ||
| clades: "defaults/clades_nextstrain.tsv" |
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I wonder if we should keep the default file named as clades.tsv, since this is what we refer to in the docs (e.g., labeling clades, the workflow reference guide, etc.) and call the derived file for the workflow something different?
If we do rename the default, we just need to update references to it in the docs.
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I had named it in analogy to clades_who, but the latter isn't really part of this workflow. I am fine with renaming it.
* add missing 19A to name translation table * rename clades file to match documentation * canonicize clade name in emergence date table
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@huddlej, did this address your concern? |
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@rneher Yeah, this looks great. Thank you! |
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ran another trial run. looks good. merging now. |
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)"
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`.
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`.
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
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
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
this PR adds