issues
search
nextstrain
/
avian-flu
Nextstrain build for avian influenza viruses
http://nextstrain.org/avian-flu
13
stars
6
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Reduce inference in cattle outbreak
#66
joverlee521
closed
1 day ago
3
Reduce inference of unknown data/location for SRA sequences
#65
joverlee521
closed
1 day ago
1
Update Andersen Lab ingest to new metadata
#64
joverlee521
closed
3 days ago
1
ingest-fauna/ingest-ncbi: Add inputs for trial_name and image
#63
joverlee521
closed
4 days ago
0
Ingest with nextclade
#62
joverlee521
opened
4 days ago
0
Add GH Action for NCBI phylogenetic workflow
#61
joverlee521
closed
1 week ago
0
Add GH Action for phylogenetic workflows
#60
joverlee521
closed
1 week ago
0
Pin pathogen-repo-ci to v0
#59
joverlee521
closed
2 weeks ago
1
Update footer with description of data sources
#58
trvrb
closed
2 weeks ago
0
ingest/joined-ncbi: Include `date_released` in metadata
#57
joverlee521
closed
2 weeks ago
0
Fixes for Andersen lab
#56
joverlee521
closed
2 weeks ago
1
h5n1-cattle-outbreak: Add Andersen lab to `data_provenance`
#55
joverlee521
closed
2 weeks ago
0
Switch Andersen lab metadata
#54
joverlee521
closed
2 weeks ago
1
ingest/andersen-lab: Switch to automated CSV file
#53
joverlee521
closed
2 weeks ago
1
Add GH Action workflows for ingest
#52
joverlee521
closed
2 weeks ago
0
ingest: Add new host from NCBI data
#51
joverlee521
closed
3 weeks ago
0
ingest: Join NCBI GenBank and Andersen Lab data
#50
joverlee521
closed
3 weeks ago
3
common.smk: Conditionally include `--no-sign-request` option
#49
joverlee521
opened
3 weeks ago
4
ingest/build-configs/ncbi: Download full NCBI dataset
#48
joverlee521
closed
3 weeks ago
2
Add uploads to S3 for NCBI and Andersen Lab ingests
#47
joverlee521
closed
3 weeks ago
1
ingest/build-configs/ncbi: Update host map
#46
joverlee521
closed
4 weeks ago
1
.gitignore: Ignore ingest/ncbi subdirectory
#45
joverlee521
closed
4 weeks ago
0
ingest: Run Nextclade as part of ingest
#44
joverlee521
opened
4 weeks ago
2
Automate ingest via GH Actions
#43
joverlee521
closed
2 weeks ago
0
ingest: Join NCBI and Andersen lab data
#42
joverlee521
closed
3 weeks ago
0
ingest: Upload NCBI/Andersen lab outputs to S3
#41
joverlee521
closed
3 weeks ago
0
Ingest from NCBI Virus + NCBI Datasets
#40
joverlee521
closed
4 weeks ago
5
WIP: Ingest from NCBI Datasets + Entrez
#39
joverlee521
closed
1 month ago
0
Swap from list of force included strains to list of excluded strains
#38
trvrb
closed
1 month ago
0
Ingest NCBI GenBank data for H5N1 outbreak
#37
joverlee521
closed
4 weeks ago
7
Ingest fixes
#36
jameshadfield
closed
1 month ago
3
Ingest extra sources
#35
jameshadfield
closed
3 weeks ago
1
Add download logic to "full genome" workflow
#34
huddlej
closed
1 month ago
1
Rn/use root of tree as reference
#33
rneher
closed
1 month ago
8
Treat missing data as Ns not gaps
#32
jameshadfield
closed
1 month ago
4
Update segment order for genome build
#31
jameshadfield
closed
1 month ago
2
Include traits and update metadata, include strains and Auspice config for genome workflow
#30
trvrb
closed
1 month ago
1
Update included and excluded strains for H5N1
#29
trvrb
closed
1 month ago
1
Ingest andersen lab
#28
joverlee521
closed
1 month ago
3
Update docs / snakemake
#27
jameshadfield
closed
1 month ago
1
Ingest Andersen Lab metadata and sequences
#26
joverlee521
closed
1 month ago
6
Annotate H5 clades through a node data JSON file instead of modifying metadata
#25
huddlej
opened
1 month ago
0
Update README.md
#24
corneliusroemer
closed
1 month ago
0
Update data provenance
#23
trvrb
closed
1 month ago
0
Download data from S3 to start workflow
#22
huddlej
closed
1 month ago
3
Full genome analysis of h5n1-cattle-outbreak
#21
jameshadfield
closed
1 month ago
2
Inline root sequence
#20
jameshadfield
closed
2 months ago
2
Allow config overrides
#19
jameshadfield
closed
2 months ago
1
Adopt Nextstrain's Snakemake style guide
#18
victorlin
opened
2 months ago
0
Specify CI target in a Snakemake rule
#17
victorlin
closed
2 months ago
1
Next