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nextstrain
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seasonal-flu
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
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Use Nextclade to assign clade labels in main phylogenetic workflow
#131
huddlej
opened
9 months ago
0
Automate monthly reports
#130
huddlej
opened
9 months ago
0
Make Markdown output for reports
#129
huddlej
closed
9 months ago
1
Update clades
#128
huddlej
closed
9 months ago
0
Revisit deploy-private-nextflu Netlify CLI version pin
#127
joverlee521
opened
10 months ago
0
Fix deploy private
#126
joverlee521
closed
10 months ago
1
Unable to run nextstrain command under 'Quickstart with GISAID data'
#125
swantan
closed
7 months ago
3
Nextclade
#124
rneher
closed
9 months ago
4
GISAID quickstart
#123
huddlej
closed
11 months ago
1
Deploy private nextflu builds to Netlify
#122
joverlee521
closed
12 months ago
2
CI: Update workflow triggers
#121
joverlee521
closed
1 year ago
0
private.nextflu.org/export: Remove translate rule output
#120
joverlee521
closed
1 year ago
1
Use new augur ancestral interface
#119
huddlej
closed
1 year ago
0
Update builds to use `--env` options
#118
joverlee521
closed
1 year ago
0
Keep reference strains in tree even if they are outliers
#117
huddlej
closed
1 year ago
0
Subclades
#116
rneher
closed
1 year ago
0
Remove AUGUR_RECURSION_LIMIT
#115
joverlee521
closed
1 year ago
0
Auto deploy public builds
#114
joverlee521
closed
1 year ago
6
Update README for refactored workflow
#113
joverlee521
closed
1 year ago
1
Example build not working. MissingRuleException
#112
limh25
closed
1 year ago
6
Use pathogen-repo-build workflow for builds
#111
joverlee521
closed
1 year ago
2
Feat/outliers
#110
rneher
closed
1 year ago
0
use stochastic polytomy resolution
#109
rneher
closed
1 year ago
0
Add rules to upload parsed sequences and metadata
#108
huddlej
closed
1 year ago
0
Upload metadata.tsv for downstream use
#107
corneliusroemer
closed
1 year ago
1
Automate builds
#106
joverlee521
closed
1 year ago
1
Feat/treeknit refactor
#105
rneher
closed
1 year ago
6
Remove `select-strains` references
#104
joverlee521
closed
1 year ago
0
Upload center-specific titers
#103
huddlej
closed
1 year ago
1
Clean up
#102
huddlej
closed
1 year ago
0
fix: adjust definition of V1A.1 with HA2 mutation to new corrected an…
#101
rneher
closed
1 year ago
0
fix: shift nucleotide coordinates for h3n2 clade files
#100
rneher
closed
1 year ago
0
config/reference_h3n2_na: Update CDS coordinates
#99
joverlee521
closed
1 year ago
2
H3N2 NA aa length is wrong
#98
ammaraziz
closed
1 year ago
6
add additional h3n2 clades
#97
rneher
closed
1 year ago
0
adjust h3n2 clade shortnames
#96
rneher
closed
1 year ago
0
max_date: Add an extra month to today's date
#95
joverlee521
closed
1 year ago
0
Clade update
#94
rneher
closed
1 year ago
0
Fix export_entropy rule: convert start to int
#93
joverlee521
closed
1 year ago
0
Update clades_h3n2_ha.tsv
#92
rneher
closed
1 year ago
2
Assign clades to nodes via tabular metadata
#91
uee9
opened
1 year ago
0
Annotate titers per node
#90
huddlej
closed
9 months ago
1
Add reference outgroup for 2y/6m builds
#89
joverlee521
closed
1 year ago
2
Instructions for custom flu dataset
#88
limh25
closed
2 years ago
1
Add Zoltar project configuration
#87
huddlej
closed
2 years ago
0
Fix age in months detection
#86
victorlin
closed
2 years ago
1
Use augur io and dates
#85
joverlee521
closed
2 years ago
1
Snakefile_WHO: skip empty region alignments
#84
joverlee521
closed
2 years ago
0
Use augur filter --min/max-date
#83
joverlee521
closed
9 months ago
1
Fix select-strains
#82
joverlee521
closed
2 years ago
0
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