Comments (3)
@corneliusroemer This is a separate issue to use the location hierarchy to help with the geolocation rules curation process. However, I'll close this issue since I want to address this issue in the new augur curate
command rather then putting the work here.
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Unfortunately, we stopped curating location hierarchies a while back when the numbers grew too big to handle. This means these location hierarchies are at best outdated and might not be very useful. We could maybe start up a fresh file for monkeypox. Another possibility would be to utilize our current curation script for use on monkeypox. Since it uses the same metadata structure, adjusting the script should not be too cumbersome.
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Has this been fixed by now @joverlee521 ? If I remember correctly, we use some sort of hierarchy now?
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Related Issues (20)
- Ingest: differentiate `date_released` and `date_submitted` HOT 1
- ENH: Don't subsample non-B.1 lineages
- Add accession as tip label option -> easier for getting exclusion accessions quickly HOT 1
- update README. HOT 1
- Additionally produce Zstd compressed outputs in ingest
- /usr/bin/bash: line 1: tsv-filter: command not found HOT 2
- `IndexError: tuple index out of range` in Snakemake file related to Nextalign rule, line 127 HOT 12
- Transmission Line Visualization Feature in Monkeypox Pipeline, Similar to the ncov Build
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- Rename repo & builds HOT 6
- CI is using an incompatible version of the Conda runtime HOT 22
- Ingest currently blocked by `fetch-from-ncbi-virus` HOT 2
- We seem to trigger each build twice after ingest HOT 1
- Reverse complement reverse-complemented sequences in ingest to reduce downstream complications
- Collection issue for things to bear in mind when moving a workflow to a folder
- Ingest: remove `reverse` column from metadata TSV HOT 1
- Potentially include year-only sequences
- `fix_tree.py` can create invalid tree HOT 1
- [phylo] CI workflow DAG includes `update_example_data`
- [phylo] traits input not passed to `augur export` HOT 1
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