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nextstrain
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rsv
Workflow for RSV analyses on Nextstrain.org
https://nextstrain.org/rsv
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#72
DOH-KGC0303
closed
2 weeks ago
2
Add .gitattributes file
#71
genehack
closed
2 months ago
0
ingest: use new augur curate commands
#70
j23414
closed
2 months ago
3
CI workflow runs are ~10 mins
#69
joverlee521
opened
2 months ago
0
Add resolutions to rsv
#68
rneher
closed
2 months ago
2
ingest: use new augur curate commands
#67
joverlee521
closed
2 months ago
0
ingest: Include `seqName` in Nextclade output
#66
joverlee521
closed
3 months ago
0
ingest failed on rule extend_metadata
#65
joverlee521
closed
3 months ago
4
ci.yaml: Pin `pathogen-repo-ci`
#64
joverlee521
closed
3 months ago
0
Rename `master` to `main`
#63
genehack
opened
3 months ago
0
Switch AWS credentials from a long-lived IAM user to short-lived role sessions
#62
tsibley
closed
4 months ago
0
inline root sequence, add pathogen json and nextclade extension
#61
rneher
closed
4 months ago
0
docs: fix documentation for newreference.py to reflect --gene behavior
#60
j23414
closed
3 months ago
1
Fix/alignment length
#59
rneher
closed
6 months ago
0
Add "--start" and "--end" arguments to newreference.py to allow for creating subgenic trees
#58
j23414
opened
6 months ago
0
Generalize the "extend-metadata.py" script for any {gene}_coverage columns
#57
j23414
opened
6 months ago
0
Add --start and --end flags to newreferences.py to allow for creating subgenic tree builds
#56
j23414
opened
6 months ago
0
Allows for CDS (as well as gene) features to generate a new gene reference
#55
j23414
closed
6 months ago
3
ingest: improve sorting of RSV A and RSV B with nextclade 3.2
#54
rneher
closed
7 months ago
0
Job AWS console link broken
#53
jameshadfield
closed
8 months ago
4
chore: fix broken links
#52
chaoran-chen
closed
4 months ago
1
Replace deprecated seq.ungap()
#51
victorlin
closed
9 months ago
0
CI failure: nextclade3 command not found
#50
jameshadfield
closed
9 months ago
2
chore(README): small changes/fixes, mostly formatting
#49
corneliusroemer
closed
9 months ago
0
fix: Update description to point to new clade nomenclature
#48
corneliusroemer
closed
9 months ago
0
Update description.md to update the clade system used
#47
corneliusroemer
closed
9 months ago
0
Nextclade v3
#46
rneher
closed
9 months ago
1
Nextclade
#45
rneher
closed
10 months ago
0
Add detailed usage docs
#44
joverlee521
opened
11 months ago
0
Sync vendored repo, update usage docs
#43
victorlin
closed
11 months ago
0
description: Update "Underlying data" section to NCBI Datasets
#42
joverlee521
closed
1 year ago
0
ingest: Conditionally include upload rule
#41
victorlin
closed
1 year ago
0
Sync vendored scripts
#40
victorlin
closed
11 months ago
3
ingest: Remove parameters related to trigger
#39
joverlee521
opened
1 year ago
0
CI: Update workflow triggers
#38
joverlee521
closed
1 year ago
1
ingest: Switch to NCBI Datasets CLI to fetch data
#37
joverlee521
closed
1 year ago
4
Ingest currently blocked by NCBI Virus changes
#36
joverlee521
closed
1 year ago
0
config/clades: remove excess whitespace
#35
joverlee521
closed
1 year ago
1
Switch to `augur curate titlecase` and `format-dates` subcommands
#34
j23414
closed
1 year ago
1
Remove deduplication on `strain`
#33
victorlin
opened
1 year ago
0
Use nextstrain/ingest
#32
victorlin
closed
1 year ago
0
Remove unused rules/scripts
#31
victorlin
closed
1 year ago
0
Add CI and example data
#30
victorlin
closed
1 year ago
1
Update usage of "accession" as the ID column
#29
victorlin
closed
1 year ago
6
fix: Treat geolocation-rules.tsv and annotations.tsv as input files
#28
j23414
closed
1 year ago
0
ENH: Add pathogen-ci to ci
#27
corneliusroemer
closed
1 year ago
0
Add pathogen-ci to ci
#26
corneliusroemer
closed
1 year ago
1
Canonicalize column order of clades tsvs
#25
corneliusroemer
closed
1 year ago
0
remove conda statement from fetch_from_genbank (the only rule that ha…
#24
rneher
closed
1 year ago
2
fix: Add `--cores` to gh actions nextstrain build
#23
corneliusroemer
closed
1 year ago
0
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