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18 Open 24 Closed
18 Open 24 Closed
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Issues list

Standardized composable configs
#79 opened Dec 10, 2024 by joverlee521
3
work needed to allow users to run analyses separate to pathogen workflows proposal Proposals that warrant further discussion
#74 opened Nov 24, 2024 by jameshadfield
5 tasks
4
Provide a generic pattern for including additional user data alongside curated data enhancement New feature or request
#72 opened Nov 8, 2024 by genehack
2
Bacterial workflow support enhancement New feature or request
#64 opened Oct 2, 2024 by genehack
@kimandrews
ingest: Add standardized steps for curating host enhancement New feature or request
#63 opened Aug 20, 2024 by joverlee521
ingest: How to handle segmented viruses
#59 opened Jul 26, 2024 by joverlee521
12
ingest: Update default config params for strain
#57 opened Jul 24, 2024 by joverlee521
3
ingest: Add build-configs for CI enhancement New feature or request
#56 opened Jul 16, 2024 by joverlee521
8
ingest: Standardize steps for adding gene coverage to metadata enhancement New feature or request
#50 opened Jul 10, 2024 by joverlee521
4
Add template for phylogenetic description.md enhancement New feature or request
#48 opened Jun 28, 2024 by joverlee521
1
Pathogen repo linter
#28 opened Feb 6, 2024 by joverlee521
How should we standardize config schema for files?
#26 opened Jan 17, 2024 by joverlee521
3
How should we standardize GitHub Action workflows per repo?
#25 opened Jan 12, 2024 by joverlee521
8
Add standard logging of config values enhancement New feature or request
#18 opened Nov 27, 2023 by joverlee521
8
Standardize output metadata fields for Nextstrain ingest
#20 opened Nov 22, 2023 by joverlee521
@joverlee521
3
Reconsider including vendored scripts in ingest template
#12 opened Oct 14, 2023 by joverlee521
2
Ingest: Support bacterial genomes enhancement New feature or request
#11 opened Oct 12, 2023 by joverlee521
Add optional BioSample rules to ingest pipeline enhancement New feature or request
#8 opened Oct 10, 2023 by joverlee521
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