Skip to content

Issues: nextstrain/ncov-ingest

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

32 Open 66 Closed
32 Open 66 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Update links for GISAID and GenBank accessions
#484 opened Dec 13, 2024 by joverlee521
3 tasks
Properly handle CSV-like TSVs
#482 opened Dec 6, 2024 by joverlee521
RKI: filter for PANGOLIN_LATEST enhancement New feature or request
#478 opened Oct 3, 2024 by joverlee521
GitHub actions log is >2hr behind actual AWS run bug Something isn't working
#474 opened Aug 22, 2024 by corneliusroemer
8
Benchmark in every rule is annoying - extra 2 lines that should not be necessary
#472 opened Aug 22, 2024 by corneliusroemer
2
Remove --stats when we upgrade to Snakemake v8
#452 opened Jun 18, 2024 by joverlee521
1
Do we need uncompress_cog_uk_metadata and compress_cog_uk_metadata?
#450 opened Jun 17, 2024 by joverlee521
1
Rename master to main blocked Dependent on external development enhancement New feature or request
#449 opened Jun 13, 2024 by genehack
1
Explore parallelizing transform-gisaid
#448 opened Jun 13, 2024 by joverlee521
GISAID workflow hitting max_session_duration
#446 opened Jun 11, 2024 by joverlee521
1 of 5 tasks
@joverlee521
8
Lock dependencies using pip-compile enhancement New feature or request
#438 opened Feb 21, 2024 by victorlin
Ingest VirusSeq data enhancement New feature or request
#421 opened Dec 7, 2023 by chaoran-chen
3
Make use of genbank's purpose_of_sampling field enhancement New feature or request
#415 opened Aug 10, 2023 by corneliusroemer
Most RKI sequences lack submission date
#410 opened Jul 11, 2023 by corneliusroemer
@corneliusroemer
1
Send error logs to Slack enhancement New feature or request
#408 opened Jun 28, 2023 by joverlee521
Add reasonable default for clade_legacy so that new clade doesn't require changes in ingest's clade-legacy-mapping.yml enhancement New feature or request
#406 opened Jun 21, 2023 by corneliusroemer
@corneliusroemer
Add Genbase sequences to open data enhancement New feature or request
#402 opened May 5, 2023 by corneliusroemer
1
ENH: Use benchmark: to find memory intensive rules enhancement New feature or request
#378 opened Dec 14, 2022 by corneliusroemer
ENH: Produce "small" metadata.tsv with only essential columns enhancement New feature or request
#376 opened Dec 13, 2022 by corneliusroemer
Nextclade refactor grab list enhancement New feature or request
#375 opened Dec 13, 2022 by corneliusroemer
2 tasks
Pull data directly from COG-UK Data enhancement New feature or request
#329 opened Jul 25, 2022 by joverlee521
2
Allow ncov-ingest to upload to non-AWS remote file paths enhancement New feature or request
#308 opened May 13, 2022 by huddlej
Allow ncov-ingest to download from non-AWS remote file paths enhancement New feature or request
#307 opened May 13, 2022 by huddlej
2
Include quick clade count after every ingest in logs enhancement New feature or request
#251 opened Dec 10, 2021 by corneliusroemer
check-locations: Columns have mixed types bug Something isn't working
#249 opened Dec 10, 2021 by ivan-aksamentov
ProTip! Follow long discussions with comments:>50.