nextstrain ncov-ingest issues

nextstrain / ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

MIT License

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issues

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Remove stuff associated with location_hierarchy

#481 victorlin opened 1 week ago
0
Replace `fetch-from-biosample` with NCBI Dataset CLI

#480 joverlee521 closed 1 month ago
2
Update README instructions for Nextclade re-runs

#479 joverlee521 closed 1 month ago
1
RKI: filter for `PANGOLIN_LATEST`

#478 joverlee521 opened 1 month ago
0
Update to NCBI Dataset v2 API

#477 joverlee521 closed 1 month ago
2
Update RKI data processing

#476 j23414 closed 2 months ago
0
Automated GenBank ingest failing

#475 joverlee521 closed 2 months ago
0
GitHub actions log is >2hr behind actual AWS run

#474 corneliusroemer opened 3 months ago
8
fix: make legacy mapping use `{clade} (Omicron)` by default

#473 corneliusroemer closed 3 months ago
3
Benchmark in every rule is annoying - extra 2 lines that should not be necessary

#472 corneliusroemer opened 3 months ago
2
The `Nextstrain_clade` column does not contain `24C`, but `?` instead.

#471 corneliusroemer closed 3 months ago
3
Map Asia/Korea/Youngin-Si to Asia/South Korea/Youngin-Si

#470 victorlin closed 3 months ago
0
Add geolocation rules for new `Korea` strains

#469 victorlin closed 3 months ago
0
Remove version columns

#468 joverlee521 opened 3 months ago
1
Surface Nextclade versions

#467 joverlee521 closed 3 months ago
2
Ignore cache if Nextclade or dataset version is different

#466 joverlee521 closed 3 months ago
4
Update vendored

#465 joverlee521 closed 4 months ago
0
Update .gitattributes with EOL settings

#464 genehack closed 4 months ago
0
Add retries to trigger rules

#463 joverlee521 closed 4 months ago
1
Add Snakemake retries to trigger jobs

#462 joverlee521 closed 4 months ago
0
Pass threads to Nextclade

#461 joverlee521 closed 4 months ago
1
Add threads to Nextclade runs

#460 joverlee521 closed 4 months ago
1
Define threads for Nextclade rules

#459 joverlee521 closed 4 months ago
8
Surface Nextclade version + Nextclade dataset version in final metadata output

#458 joverlee521 closed 3 months ago
10
Ignore Nextclade cache on new Nextclade version or dataset version

#457 joverlee521 closed 3 months ago
2
Metadata includes Nextstrain clades in the `Nextclade_pango` column

#456 joverlee521 closed 4 months ago
12
Fetch from COG-UK failing

#455 joverlee521 closed 4 months ago
3
Update vendored scripts

#454 joverlee521 closed 4 months ago
0
build(deps): bump docker/build-push-action from 5 to 6

#453 dependabot[bot] closed 3 months ago
0
Remove `--stats` when we upgrade to Snakemake v8

#452 joverlee521 opened 5 months ago
1
Add benchmark and `--stats`

#451 joverlee521 closed 5 months ago
1
Do we need `uncompress_cog_uk_metadata` and `compress_cog_uk_metadata`?

#450 joverlee521 opened 5 months ago
1
Rename `master` to `main`

#449 genehack opened 5 months ago
1
Explore parallelizing `transform-gisaid`

#448 joverlee521 opened 5 months ago
0
Bump CPUs for fetch-and-ingest workflows

#447 joverlee521 closed 5 months ago
4
GISAID workflow hitting max_session_duration

#446 joverlee521 opened 5 months ago
8
Switch AWS credentials from a long-lived IAM user to short-lived role sessions

#445 tsibley closed 5 months ago
0
fetch-and-ingest: Explicitly test FETCH_FROM_DATABASE

#444 joverlee521 closed 7 months ago
0
Update clade-legacy-mapping.yml with 24A and 24B

#443 corneliusroemer closed 7 months ago
0
trigger_rebuild_pipeline: Update inputs to match ncov builds

#442 joverlee521 closed 8 months ago
1
feat(nextclade): workaround for https://github.com/nextstrain/nextclade/issues/1422 no longer needed

#441 corneliusroemer closed 4 months ago
1
Overhaul GH Action workflows

#440 joverlee521 closed 8 months ago
9
Fix image

#439 joverlee521 closed 9 months ago
2
Lock dependencies using pip-compile

#438 victorlin opened 9 months ago
0
Remove unused variables and refactor `GENE_LIST`

#437 joverlee521 closed 9 months ago
1
Bump cryptography from 38.0.3 to 42.0.4

#436 dependabot[bot] closed 9 months ago
1
feat: switch to nextclade3, by downloading "latest" binary

#435 corneliusroemer closed 9 months ago
1
Bump cryptography from 38.0.3 to 42.0.2

#434 dependabot[bot] closed 9 months ago
1
Bump cryptography from 38.0.3 to 42.0.0

#433 dependabot[bot] closed 9 months ago
1
Bump aiohttp from 3.8.3 to 3.9.2

#432 dependabot[bot] closed 9 months ago
1