nextstrain pathogen-repo-guide issues

nextstrain / pathogen-repo-guide

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ingest: Add example build-config/ci/config.yaml

#71 genehack opened 1 week ago
0
Update nextclade workflow docs for v3

#70 joverlee521 closed 2 weeks ago
1
Migrate to Nextclade v3

#69 joverlee521 closed 2 weeks ago
0
Adds a recommended `is_lab_host` column to the ingested metadata.tsv file

#68 j23414 closed 4 weeks ago
0
ingest: Nextclade merge updates

#67 tsibley closed 1 month ago
0
ingest: Properly handle CSV-like TSVs

#66 joverlee521 opened 1 month ago
0
ingest: Updates for `augur curate` and `augur merge`

#65 joverlee521 closed 1 month ago
1
Bacterial workflow support

#64 genehack opened 1 month ago
0
ingest: Add standardized steps for curating host

#63 joverlee521 opened 2 months ago
0
Link to Nextstrain docs

#62 joverlee521 closed 2 months ago
0
Adding ingest guide to documentation

#61 miparedes closed 2 months ago
1
ingest: Add lab host fields from NCBI Datasets

#60 joverlee521 closed 4 weeks ago
1
ingest: How to handle segmented viruses

#59 joverlee521 opened 3 months ago
12
Missing comma in `fetch_ncbi_dataset_package` rule causing syntax error

#58 BryanTegomoh closed 3 months ago
5
ingest: Update default config params for strain

#57 joverlee521 opened 3 months ago
3
ingest: Add build-configs for CI

#56 joverlee521 opened 3 months ago
7
ingest/nextclade: Replace `csvtk`

#55 joverlee521 closed 1 month ago
2
Ingest nextclade updates

#54 joverlee521 closed 3 months ago
2
ingest: use new augur curate commands

#53 joverlee521 closed 3 months ago
2
Fix typo in `ingest/rules/curate.smk`

#52 kimandrews closed 3 months ago
0
ingest: Use of `data` vs `results` directories

#51 joverlee521 closed 3 months ago
5
ingest: Standardize steps for adding gene coverage to metadata

#50 joverlee521 opened 4 months ago
4
ingest: use new augur curate commands

#49 joverlee521 closed 3 months ago
0
Add template for phylogenetic `description.md`

#48 joverlee521 opened 4 months ago
1
Updates to use of Nextclade in ingest workflow

#47 joverlee521 closed 3 months ago
0
Propagate `.gitattributes` to Nextstrain pathogen repos

#46 joverlee521 closed 3 months ago
5
Add docs for internal Nextstrain team

#45 joverlee521 closed 4 months ago
0
Update `pathogen-repo-ci` to "generic"/"smart" workflow

#44 genehack closed 5 months ago
1
Add pre-commit-config and GHA [#42]

#43 genehack closed 5 months ago
0
Add pre-commit-config.yaml, pre-commit GHA, and cleanup existing files

#42 genehack closed 5 months ago
1
Misc tpyoes

#41 genehack closed 5 months ago
3
ingest: Create new accession field without version

#40 joverlee521 closed 6 months ago
2
ingest: GenBank accession should not include version number

#39 joverlee521 closed 6 months ago
1
ingest: Provide target for raw metadata from NCBI Datasets

#38 joverlee521 closed 7 months ago
1
Add .gitattibutes to force line endings to be LF

#37 joverlee521 closed 7 months ago
1
ingest/build-configs/nextstrain-automation: Add README

#36 joverlee521 closed 7 months ago
1
ingest/nextstrain-automation: Fix upload_to_s3

#35 joverlee521 closed 8 months ago
0
ingest: Move Nextclade configs to separate YAML

#34 joverlee521 closed 8 months ago
1
ingest: Add default values to config.yaml

#33 joverlee521 closed 8 months ago
2
ingest: Move intermediate files to `data` directory

#32 joverlee521 closed 8 months ago
0
Update ingest to output to data/ for intermediate files

#31 joverlee521 closed 8 months ago
0
Provide a no-curation option for NCBI Ingest

#30 j23414 closed 7 months ago
1
Add top level nextstrain-pathogen.yaml file

#29 joverlee521 closed 9 months ago
0
Pathogen repo linter

#28 joverlee521 opened 9 months ago
0
Rename "profiles" to "build-configs"

#27 joverlee521 closed 9 months ago
10
How should we standardize config schema for files?

#26 joverlee521 opened 9 months ago
3
How should we standardize GitHub Action workflows per repo?

#25 joverlee521 opened 10 months ago
8
profiles: rename defaults.yaml to profiles_config.yaml

#24 joverlee521 closed 9 months ago
7
Version nextclade binary for transition, i.e. nextclade -> nextclade2

#23 corneliusroemer closed 9 months ago
0
handle bare quotes in fields

#22 j23414 closed 11 months ago
1