nextstrain mpox issues - Githubissues

nextstrain / mpox

Nextstrain build for mpox virus

https://nextstrain.org/mpox

MIT License

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issues

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Newest Most commented Recently updated Oldest Least commented Least recently updated

ingest: use new augur curate commands

#262 joverlee521 opened 1 day ago
0
Trim reuse text

#261 victorlin closed 3 days ago
0
Sync .gitattributes with pathogen-repo-guide

#260 victorlin closed 1 week ago
1
Update phylogenetic GH Action workflows

#259 joverlee521 opened 2 weeks ago
0
Switch CI to `pathogen-repo-ci` action [#257]

#258 genehack closed 3 weeks ago
2
Convert CI to "modern" `pathogen-repo-ci`

#257 genehack closed 3 weeks ago
0
Switch AWS credentials from a long-lived IAM user to short-lived role sessions

#256 tsibley closed 4 weeks ago
0
Allow addition of unreleased INRB data

#255 jameshadfield opened 1 month ago
0
Add Clade-I build

#254 jameshadfield closed 2 weeks ago
1
[pre-commit.ci] pre-commit autoupdate

#253 pre-commit-ci[bot] opened 1 month ago
0
[phylo] Reconnect traits to export

#252 joverlee521 closed 1 month ago
0
[phylo] traits input not passed to `augur export`

#251 joverlee521 closed 1 month ago
1
[pre-commit.ci] pre-commit autoupdate

#250 pre-commit-ci[bot] closed 1 month ago
0
ingest: Remove `inrb` source from config.yaml

#249 joverlee521 closed 2 months ago
1
Remove `inrb.ndjson` as sequences now available via NCBI

#248 corneliusroemer closed 2 months ago
0
Fix fstring format

#247 joverlee521 closed 2 months ago
1
Re-eneable snakefmt in pre-commit

#246 corneliusroemer closed 2 months ago
0
Use nextclade3 for phylogenetic workflow

#245 corneliusroemer closed 2 months ago
0
Tweak clade I definitions and exclude misaligned/overdiverged

#244 corneliusroemer closed 2 months ago
0
Add submission date to the INRB sequences

#243 j23414 closed 2 months ago
1
Ingest INRB data with permission

#242 j23414 closed 2 months ago
6
Add new lineages B.1.21, B.1.22, C.1.1 to phylogenetic

#241 corneliusroemer closed 2 months ago
0
Update nextclade workflow for new clades B.1.21, B.1.22, C.1.1

#240 corneliusroemer closed 2 months ago
0
Fix trial rebuilds

#239 joverlee521 closed 4 months ago
1
Phylogenetic updates to match pathogen-repo-guide

#238 joverlee521 closed 4 months ago
2
[phylo] CI workflow DAG includes `update_example_data`

#237 joverlee521 opened 4 months ago
0
[pre-commit.ci] pre-commit autoupdate

#236 pre-commit-ci[bot] closed 2 months ago
0
dev: Use preview version of our centralized pathogen-repo-build.yaml workflow

#235 tsibley closed 4 months ago
1
Update ingest to pathogen-repo-template

#234 joverlee521 closed 5 months ago
4
build(deps): bump actions/checkout from 3 to 4

#233 dependabot[bot] closed 5 months ago
0
`fix_tree.py` can create invalid tree

#232 joverlee521 opened 5 months ago
1
Potentially include year-only sequences

#231 corneliusroemer opened 5 months ago
0
Use mutations rather than mutations-per-site for clade IIb/B.1 builds

#230 corneliusroemer closed 5 months ago
0
Add Quickstart section to the top level README

#229 joverlee521 closed 5 months ago
0
ingest: download Nextclade V2 dataset

#228 joverlee521 closed 5 months ago
1
Version nextalign binary for transition

#227 victorlin closed 5 months ago
1
Version nextclade binary for transition, i.e. nextclade -> nextclade2

#226 corneliusroemer closed 5 months ago
2
Add Nextclade dataset workflow in `/nextclade` dir

#225 corneliusroemer closed 7 months ago
0
fetch-and-ingest-branch: Send Slack notications to test channel

#224 joverlee521 closed 7 months ago
1
Fix ingest uploads

#223 joverlee521 closed 7 months ago
2
Ingest updates

#222 joverlee521 closed 8 months ago
0
.github/workflows: Use centralized SLACK_CHANNELS variable

#221 joverlee521 closed 8 months ago
1
Rename instances of "monkeypox" to "mpox"

#220 trvrb closed 8 months ago
10
Move the NCBI field map to config

#219 j23414 closed 8 months ago
0
GitHub Action workflows clean up

#218 joverlee521 closed 8 months ago
2
Move ncbi taxon id to config

#217 j23414 closed 8 months ago
0
[wip] Attempt to eradicate confounding of release and submission

#216 j23414 opened 8 months ago
0
Move s3_dst config to top level config

#215 j23414 closed 8 months ago
1
Add CI profile to run CI build

#214 joverlee521 closed 8 months ago
1
Styleguide: Avoid the message rule attribute

#213 j23414 closed 8 months ago
0