Latest alignment to pathogen-repo-guide in 2024 #89
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This commit updates the `ingest` directory to match the latest version of the: https://github.com/nextstrain/pathogen-repo-guide/tree/b4001735fa55448f1426ff90cca93c667ca121ce/ingest
Since auspice automatically detects "authors" and we prefer the abbreviated authors list displayed, change "abbr_authors" to "authors" and "authors" to "full_authors". This matches the pathogen-repo-guide
To match the pathogen repo guide, change: * `genbank_accession` to `accession` * `genbank_accession_rev` to `accession_version` There should be a subsequent change in the phylogenetic workflow
To be more consistent with the pathogen-repo-guide and the ingest workflow
Use the combination of `accession` and `url` fields in the phylogenetic build. This change follows a similar change to the ingest workflow.
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Ended up fixing the frequencies plot in #88 so these commits will be part of that PR |
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Description of Proposed Changes
While working on this repository to add the frequency panel, I took the opportunity to update the workflow to align with the latest version of the Pathogen Repo Guide.
The following commits were extracted from the larger frequency PR (#88) and are included here:
Changes to Conform to the Pathogen Repo Guide
Ingest Workflow:
authorstofull_authorsandabbr_authorstoauthors.genbank_accessiontoaccessionandgenbank_accession_revtoaccession_version.urlcolumn.release_datetodate_releasedandupdate_datetodate_updated.is_lab_hostcolumn.Phylogenetic Workflow:
*/configdirectories to*/defaults.is_lab_hostfrom downstream analysis.Related Issues
configtodefaults#77.Checklist