Align SC2 with new clades tsvs in ncov#42
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corneliusroemer merged 1 commit intomasterfrom May 22, 2023
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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)"
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I forgot to add a prospective CHANGELOG entry for the datasets and just noticed now that this change has downstream implications for ncov-ingest |
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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`.
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corneliusroemer
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Jun 20, 2023
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`.
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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)"