Include year_letter_clade & more in metadata #373
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We currently output only composite clade names, e.g. `21L (Omicron)` Nextclade now produces also atomic clades, that are Nextstrain and WHO only: `21L` and `Omicron`. Nextclade will at some point switch "clade" from `legacy` to `Nextstrain` This commit insulates ingest-metadata from this upcoming change by using `clade_legacy` in place of `clade` in the column_map as source of `Nextstrain_clade`. This commit also adds: - `year_letter_clade` sourced from `clade_nextstrain` - `who_variant` sourced from `clade_who` - `clade_display_name`: calculated as `21L (Omicron)`/`20C`
rneher
approved these changes
Dec 13, 2022
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We currently output only composite clade names, e.g.
21L (Omicron)Nextclade now produces also atomic clades,
that are Nextstrain and WHO only:
21LandOmicron.Nextclade will at some point switch "clade" from
legacytoNextstrainThis commit insulates ingest-metadata from this upcoming change
by using
clade_legacyin place ofcladein the column_map assource of
Nextstrain_clade.At some point we may drop/deprecate the complex
Nextstrain_clade- or keep it for backwards compatibility.For new scripts, one should use
year_letter_cladefrom now on, this is the best unique cladekeyfor the Nextstrain clade schema.This commit also adds:
year_letter_cladesourced fromclade_nextstrainwho_variantsourced fromclade_whoclade_display_name: calculated as21L (Omicron)/20CTested using
config/debug_sample_genbank.yamland it worked thereTest runs:
3864fece-2ed7-496a-88cf-603f47bcf708a7ded173-ade8-43aa-91fd-0b24d273aa31