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nextstrain
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mpox
Nextstrain build for mpox virus
https://nextstrain.org/mpox
MIT License
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Add Quickstart section to the top level README
#229
joverlee521
closed
8 months ago
0
ingest: download Nextclade V2 dataset
#228
joverlee521
closed
8 months ago
1
Version nextalign binary for transition
#227
victorlin
closed
8 months ago
1
Version nextclade binary for transition, i.e. nextclade -> nextclade2
#226
corneliusroemer
closed
8 months ago
2
Add Nextclade dataset workflow in `/nextclade` dir
#225
corneliusroemer
closed
10 months ago
0
fetch-and-ingest-branch: Send Slack notications to test channel
#224
joverlee521
closed
10 months ago
1
Fix ingest uploads
#223
joverlee521
closed
10 months ago
2
Ingest updates
#222
joverlee521
closed
11 months ago
0
.github/workflows: Use centralized SLACK_CHANNELS variable
#221
joverlee521
closed
11 months ago
1
Rename instances of "monkeypox" to "mpox"
#220
trvrb
closed
11 months ago
10
Move the NCBI field map to config
#219
j23414
closed
11 months ago
0
GitHub Action workflows clean up
#218
joverlee521
closed
11 months ago
2
Move ncbi taxon id to config
#217
j23414
closed
11 months ago
0
[wip] Attempt to eradicate confounding of release and submission
#216
j23414
opened
11 months ago
0
Move s3_dst config to top level config
#215
j23414
closed
11 months ago
1
Add CI profile to run CI build
#214
joverlee521
closed
11 months ago
1
Styleguide: Avoid the message rule attribute
#213
j23414
closed
11 months ago
0
ingest: Link to vendored/README.md for instructions on vendoring
#212
victorlin
closed
11 months ago
0
doc: ncbi datasets
#211
j23414
closed
11 months ago
1
Remove `reverse` column, associated script, and references
#210
joverlee521
opened
11 months ago
0
Ingest: remove `reverse` column from metadata TSV
#209
joverlee521
closed
2 months ago
1
fix: script moved to phylogenetic dir
#208
j23414
closed
11 months ago
1
Replace join metadata and clades script with csvtk and tsv append
#207
j23414
closed
11 months ago
1
Remove extra actionlint
#206
joverlee521
closed
12 months ago
1
[pre-commit.ci] pre-commit autoupdate
#205
pre-commit-ci[bot]
closed
10 months ago
0
Update dev docs
#204
victorlin
closed
1 year ago
1
Pin pathogen-repo-commit till `build-dir` support is on main
#203
corneliusroemer
closed
1 year ago
0
Collection issue for things to bear in mind when moving a workflow to a folder
#202
corneliusroemer
opened
1 year ago
0
fix: correct vendored path in notify-on-* scripts after move and build action args
#201
corneliusroemer
closed
1 year ago
3
general precommit lints
#200
corneliusroemer
closed
1 year ago
0
chore: builds are robust now, can deploy straight to nextstrain-data
#199
corneliusroemer
closed
1 year ago
0
Move phylogenetic workflow from top-level to folder `phylogenetic`
#198
corneliusroemer
closed
1 year ago
0
Add actionlint (for Github actions) to pre-commit
#197
corneliusroemer
closed
1 year ago
1
Add yamlfmt to pre-commit (and format with it)
#196
corneliusroemer
closed
1 year ago
1
Add pre-commit to CI lint action
#195
corneliusroemer
closed
1 year ago
1
Update README
#194
victorlin
closed
1 year ago
0
Add pyproject.toml for sane `snakefmt` excludes, add `.git/` to `.gitignore`
#193
corneliusroemer
closed
1 year ago
0
Reverse complement reverse-complemented sequences in ingest to reduce downstream complications
#192
corneliusroemer
opened
1 year ago
0
Fix reverse complement script, use-fft again, exclude unalignable sequences
#191
corneliusroemer
closed
1 year ago
0
Use pathogen-repo-build workflow for builds
#190
corneliusroemer
closed
1 year ago
3
ingest: Add `profiles/default` to make `-c1 --ri` unnecessary
#189
corneliusroemer
closed
1 year ago
0
Move phylogenetic workflow to folder
#188
corneliusroemer
closed
1 year ago
2
chore: apply snakefmt
#187
corneliusroemer
closed
1 year ago
6
We seem to trigger each build twice after ingest
#186
corneliusroemer
closed
1 year ago
1
Reorganize config and rules around filter/subsampling
#185
victorlin
closed
1 year ago
1
Switch to `augur curate titlecase` and `format-dates` subcommands
#184
j23414
closed
1 year ago
0
Put each build's specific config files in folders
#183
corneliusroemer
closed
1 year ago
0
Use centralized script for transform strain names
#182
j23414
closed
1 year ago
1
Update example data (new lineages have been designated)
#181
corneliusroemer
closed
1 year ago
0
description: Update "Underlying data" section to NCBI Datasets
#180
joverlee521
closed
1 year ago
0
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