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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Update vendored scripts

#454 joverlee521 opened 1 day ago
0
build(deps): bump docker/build-push-action from 5 to 6

#453 dependabot[bot] opened 1 week ago
0
Remove `--stats` if/when we upgrade to Snakemake v8

#452 joverlee521 opened 2 weeks ago
0
Add benchmark and `--stats`

#451 joverlee521 closed 2 weeks ago
1
Do we need `uncompress_cog_uk_metadata` and `compress_cog_uk_metadata`?

#450 joverlee521 opened 2 weeks ago
1
Rename `master` to `main`

#449 genehack opened 3 weeks ago
0
Explore parallelizing `transform-gisaid`

#448 joverlee521 opened 3 weeks ago
0
Bump CPUs for fetch-and-ingest workflows

#447 joverlee521 closed 3 weeks ago
4
GISAID workflow hitting max_session_duration

#446 joverlee521 opened 3 weeks ago
7
Switch AWS credentials from a long-lived IAM user to short-lived role sessions

#445 tsibley closed 4 weeks ago
0
fetch-and-ingest: Explicitly test FETCH_FROM_DATABASE

#444 joverlee521 closed 2 months ago
0
Update clade-legacy-mapping.yml with 24A and 24B

#443 corneliusroemer closed 3 months ago
0
trigger_rebuild_pipeline: Update inputs to match ncov builds

#442 joverlee521 closed 4 months ago
1
feat(nextclade): workaround for https://github.com/nextstrain/nextclade/issues/1422 no longer needed

#441 corneliusroemer opened 4 months ago
0
Overhaul GH Action workflows

#440 joverlee521 closed 4 months ago
9
Fix image

#439 joverlee521 closed 4 months ago
2
Lock dependencies using pip-compile

#438 victorlin opened 4 months ago
0
Remove unused variables and refactor `GENE_LIST`

#437 joverlee521 closed 4 months ago
1
Bump cryptography from 38.0.3 to 42.0.4

#436 dependabot[bot] closed 4 months ago
1
feat: switch to nextclade3, by downloading "latest" binary

#435 corneliusroemer closed 4 months ago
1
Bump cryptography from 38.0.3 to 42.0.2

#434 dependabot[bot] closed 4 months ago
1
Bump cryptography from 38.0.3 to 42.0.0

#433 dependabot[bot] closed 4 months ago
1
Bump aiohttp from 3.8.3 to 3.9.2

#432 dependabot[bot] closed 4 months ago
1
Bump cryptography from 38.0.3 to 41.0.6

#431 dependabot[bot] closed 5 months ago
1
Bump urllib3 from 1.26.12 to 1.26.18

#430 dependabot[bot] closed 4 months ago
1
Use built-in Snakemake `retries` directive

#429 joverlee521 closed 5 months ago
1
Bump docker/login-action from 2 to 3

#428 dependabot[bot] closed 5 months ago
0
Bump docker/setup-buildx-action from 2 to 3

#427 dependabot[bot] closed 4 months ago
0
Bump docker/build-push-action from 3 to 5

#426 dependabot[bot] closed 4 months ago
0
Bump actions/checkout from 3 to 4

#425 dependabot[bot] closed 5 months ago
1
Fix upload diff race

#424 joverlee521 closed 5 months ago
2
Race condition between diff and uploads to S3

#423 joverlee521 closed 5 months ago
0
Download nextclade 2.14.0 binary instead of latest

#422 corneliusroemer closed 5 months ago
1
Ingest VirusSeq data

#421 chaoran-chen opened 7 months ago
3
Replace `fetch-from-biosample` with NCBI Datasets output

#420 joverlee521 opened 8 months ago
0
Sync vendored scripts

#419 victorlin closed 8 months ago
0
Add build dir for notify-on-job-start

#418 joverlee521 closed 10 months ago
2
Remove unused notify-on-metadata-change

#417 victorlin closed 10 months ago
0
Fix docker build

#416 victorlin closed 4 months ago
11
Make use of genbank's `purpose_of_sampling` field

#415 corneliusroemer opened 10 months ago
0
Map clades not in clade-legacy-mapping.yml to itself

#414 corneliusroemer opened 11 months ago
0
Unable to build Docker image

#413 victorlin closed 4 months ago
1
Use nextstrain/ingest

#412 victorlin closed 10 months ago
0
Remove unused `run-nextclade-full` scripts and GH Action workflows

#411 joverlee521 closed 11 months ago
0
Most RKI sequences lack submission date

#410 corneliusroemer opened 12 months ago
1
Fix/rki tsv csv

#409 rneher closed 12 months ago
4
Send error logs to Slack

#408 joverlee521 opened 1 year ago
0
Add recombinant to legacy mapping

#407 emmahodcroft closed 1 year ago
3
Add reasonable default for clade_legacy so that new clade doesn't require changes in ingest's `clade-legacy-mapping.yml`

#406 corneliusroemer opened 1 year ago
0
Fix: add clade_legacy back via mapping

#405 corneliusroemer closed 1 year ago
3