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nextstrain
/
augur
Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
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curate apply-geolocation-rules: Allow rule overrides
#1648
joverlee521
opened
1 day ago
0
Update cram tests
#1647
victorlin
closed
3 days ago
1
index: Allow FileNotFoundError to be handled at the top level
#1646
victorlin
closed
4 days ago
2
Add examples for weighted sampling with multiple columns including month/week
#1645
victorlin
opened
1 week ago
0
Augur index may always report sequence file is missing even if output dir is missing?
#1644
emmahodcroft
closed
4 days ago
2
Also accept "region" as synonym of "source" for gb files?
#1643
corneliusroemer
opened
1 week ago
1
Improve rendering of CLI documentation
#1642
victorlin
opened
1 week ago
0
CLI: Use raw descriptions
#1641
victorlin
opened
1 week ago
0
Register subparsers recursively
#1640
victorlin
opened
1 week ago
0
DEV_DOCS: Document the shared Cram setup scripts
#1639
victorlin
closed
1 week ago
0
CI/release: Run tests on build artifacts
#1638
victorlin
opened
1 week ago
0
Use shared setup script for all Cram tests
#1637
victorlin
closed
1 week ago
0
Set pipefail for Cram tests
#1636
victorlin
closed
2 days ago
1
Add escape hatch for the "Augur version incompatibility detected" error
#1635
corneliusroemer
opened
1 week ago
2
Run release from CI workflow
#1634
victorlin
closed
1 week ago
1
Release workflow doesn't run tests successfully but continues anyway
#1633
tsibley
closed
1 week ago
2
merge: Omit generated source columns by default
#1632
tsibley
closed
2 weeks ago
3
merge: Support sequences without cross-checking
#1631
victorlin
closed
1 day ago
1
Improve help text of CLI options
#1630
victorlin
opened
2 weeks ago
3
parse: Prefer `strain` over `name` as sequence ID field
#1629
victorlin
closed
2 weeks ago
1
`augur merge` is slow to read in metadata
#1628
tsibley
opened
3 weeks ago
0
Set pipefail for cram tests
#1627
victorlin
closed
2 days ago
5
Augur traits error
#1626
vanessazubach
closed
3 weeks ago
2
merge: Support changing the names of, or omitting entirely, the generated source columns
#1625
tsibley
closed
3 weeks ago
11
Fix tests for `augur merge`
#1624
tsibley
closed
4 weeks ago
0
Keep deprecation entries consistent
#1623
victorlin
closed
1 month ago
0
filter: Deprecate `--output` and `-o`
#1622
victorlin
opened
1 month ago
1
CI: linkcheck fails occasionally due to fasttree link
#1621
corneliusroemer
closed
1 month ago
4
Release: changelog can be out-of-sync
#1620
victorlin
opened
1 month ago
4
Fix changelog
#1619
victorlin
closed
1 month ago
0
Properly upload coverage file with upload-artifact v4.4.0
#1618
victorlin
closed
1 month ago
4
merge: Import metadata files concurrently?
#1617
tsibley
opened
1 month ago
0
CI: codecov artifact download failing
#1616
victorlin
closed
1 month ago
1
Allow spaces in BEAST annotations mk2
#1615
jameshadfield
closed
1 month ago
1
Align fractional sequences per group conversion methods
#1614
victorlin
opened
1 month ago
0
filter: Error on sequence duplicates
#1613
victorlin
closed
2 weeks ago
4
Revise docs for v25 features to add `versionadded` directives
#1612
genehack
opened
1 month ago
0
Legacy editable installs are deprecated
#1611
genehack
opened
1 month ago
0
Allow spaces in BEAST annotations
#1610
watronfire
closed
1 month ago
2
Spaces in BEAST annotations cause error
#1609
watronfire
closed
1 month ago
1
merge: Ignore the user's ~/.sqliterc file, if any
#1608
tsibley
closed
1 month ago
1
filter: Prefer "output sequences" over "output"?
#1607
victorlin
opened
1 month ago
2
Pin deepdif <8.0.0
#1606
victorlin
closed
1 month ago
1
CI failing on JSON diff
#1605
victorlin
closed
1 month ago
0
Clarify missing column messages
#1604
victorlin
closed
1 month ago
1
merge: Uncaught error with user-defined `.sqliterc`
#1603
victorlin
closed
1 month ago
1
filter: `--output-sequences` silently allows duplicates
#1602
victorlin
closed
2 weeks ago
0
merge: Support sequences with cross-checking
#1601
victorlin
opened
1 month ago
1
augur ancestral - IndexError when using wrong (shorter) reference
#1600
ammaraziz
opened
1 month ago
0
Use exact fractional sequences per group
#1599
victorlin
closed
1 month ago
6
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