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24 Open 53 Closed
24 Open 53 Closed
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Issues list

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
Replace fetch-from-biosample with NCBI Datasets output enhancement New feature or request
#420 opened Oct 10, 2023 by joverlee521
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
Revisit fetch from GISAID enhancement New feature or request
#242 opened Dec 3, 2021 by joverlee521
2
Profile ncov-ingest enhancement New feature or request
#240 opened Nov 30, 2021 by joverlee521
2
Use idiomatic features of Snakemake enhancement New feature or request
#239 opened Nov 29, 2021 by huddlej
1 of 6 tasks
GISAID ingest keeps running out of memory bug Something isn't working
#217 opened Oct 1, 2021 by eharkins
1
Location hierarchy formatting issues bug Something isn't working
#78 opened Jul 8, 2020 by kairstenfay
@eharkins
16
Additional metadata & annotations validations
#61 opened Jun 5, 2020 by kairstenfay
1 task
Add too-short sequences to new exclude.txt
#45 opened May 12, 2020 by kairstenfay
Run ./bin/check-annotations as CI (or similar) enhancement New feature or request
#39 opened May 1, 2020 by jameshadfield
1
@kairstenfay
11
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