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# Currently accepts any characters because we do not have a clear standard for strain names across pathogens
strain_regex: "^.+$"
# Back up strain name field to use if "strain" doesn"t match regex above
strain_backup_fields: ["accession"]
This is a historical artifact from when augur required the strain/name column as a metadata id column. Now that we support arbitrary --metadata-id-column across subcommands since Augur 22.1.0, these default config params seem to do more harm than good (e.g. nextstrain/augur#1556 (comment)).
Possible solutions
Remove the default backup field.
Remove augur curate transform-strain-name and related config params completely since they aren't doing much here if we remove the default backup field.
The text was updated successfully, but these errors were encountered:
I slightly lean towards [1] in case NCBI Datasets does start to output the strain field, then we can use strain and isolate-lineage as the backup field.
Current default configs for
strain
requires it to be a non-empty string withaccession
as the backup field.pathogen-repo-guide/ingest/defaults/config.yaml
Lines 65 to 69 in 89b3c5d
This is a historical artifact from when augur required the strain/name column as a metadata id column. Now that we support arbitrary
--metadata-id-column
across subcommands since Augur 22.1.0, these default config params seem to do more harm than good (e.g. nextstrain/augur#1556 (comment)).Possible solutions
augur curate transform-strain-name
and related config params completely since they aren't doing much here if we remove the default backup field.The text was updated successfully, but these errors were encountered: