nextstrain seasonal-flu issues

nextstrain / seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds

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issues

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Exclude sequences with unusual collection dates

#175 joverlee521 opened 2 weeks ago
2
Run pathogen-embed on HA/NA alignments to flag putative reassortant clades

#174 huddlej opened 1 month ago
0
Summarize haplotype coverage by titer references using frequencies per haplotype from all available data

#173 huddlej closed 4 weeks ago
0
Add representative samples from early clades to "broad" H1N1pdm HA Nextclade dataset

#172 huddlej closed 1 month ago
0
Nextclade dataset for "broad" H1N1pdm HA misassigns early clade labels

#171 huddlej closed 1 month ago
0
ci.yaml: Pin `pathogen-repo-ci`

#170 joverlee521 closed 2 months ago
0
Rename `master` to `main`

#169 genehack opened 2 months ago
0
deploy-private-nextflu: Assume AWS role for short-lived credentials

#168 joverlee521 closed 2 months ago
0
Switch AWS credentials from a long-lived IAM user to short-lived role sessions

#167 tsibley closed 2 months ago
0
inline root sequence

#166 rneher closed 2 months ago
0
Upload trigger matrix

#165 joverlee521 closed 3 months ago
1
Use existing public 2y builds as “representative” trees in our reports

#164 huddlej opened 3 months ago
0
Use a narrative template file to stub out a date-specific narrative for a given set of dated builds

#163 huddlej opened 3 months ago
0
Plot counts per lineage by region with matplotlib instead of altair

#162 huddlej closed 3 months ago
0
Use metadata from NA segment in joined metadata when HA segment isn't available

#161 huddlej opened 4 months ago
0
Add isolate_id field to metadata

#160 huddlej closed 4 months ago
0
Automate deployment of private nextflu.org site

#159 joverlee521 opened 4 months ago
0
Add GitHub Action for Nextclade annotations

#158 huddlej closed 4 months ago
3
Trigger nextflu-private builds from upload action

#157 huddlej closed 5 months ago
1
Update Suffolk lat/longs

#156 joverlee521 opened 5 months ago
0
"Suffolk" in `lat_longs.tsv` points to somewhere unexpected

#155 fanninpm opened 5 months ago
1
Download clade definitions from GitHub

#154 huddlej closed 6 months ago
0
profiles/nextstrain-public: Update build/auspice names

#153 joverlee521 closed 4 months ago
5
Rename public nextstrain builds to `seasonal-flu`

#152 joverlee521 closed 4 months ago
0
GISAID Quickstart: remove Conda runtime specific command

#151 joverlee521 closed 6 months ago
0
Add measurements panel for Welsh et al. escape scores

#150 huddlej opened 6 months ago
0
Running issue nextstrain pipeline

#149 sekhwal opened 6 months ago
18
Create PA-h3n2

#148 sekhwal closed 6 months ago
1
Integrating FASTA Sequence into Influenza A/H3N2 Evolution Analysis and Visualizing in Nextclade

#147 sekhwal closed 6 months ago
6
nextstrain.yaml: Update to Nextclade v3

#146 joverlee521 closed 6 months ago
0
Nextclade3 update

#145 rneher closed 6 months ago
0
Filter low-quality sequences by Nextclade QC status

#144 huddlej opened 6 months ago
0
Bump actions/setup-node from 3 to 4

#143 dependabot[bot] closed 6 months ago
0
Bump actions/checkout from 3 to 4

#142 dependabot[bot] closed 6 months ago
0
Version nextalign binary for transition

#141 victorlin closed 7 months ago
1
Automatically deploy dated builds to nextflu-private group

#140 huddlej closed 7 months ago
0
Add rules to the nextflu-private workflow to rename Auspice JSONs based on the build date and deploy the JSONs to the Nextstrain group

#139 huddlej closed 7 months ago
0
Add Auspice JSON colorings for HA/NA accessions

#138 huddlej closed 7 months ago
2
Export GISAID accessions from metadata into Auspice JSONs

#137 huddlej closed 7 months ago
0
Update subclades

#136 rneher closed 8 months ago
0
Add Welsh et al. epitope sites and escape scores

#135 huddlej closed 6 months ago
0
Version nextclade binary for transition, i.e. nextclade -> nextclade2

#134 corneliusroemer closed 7 months ago
0
Dmsa phenotype

#133 jgallowa07 closed 8 months ago
1
Add h3n2/na segment length to GFF

#132 jameshadfield closed 8 months ago
0
Use Nextclade to assign clade labels in main phylogenetic workflow

#131 huddlej opened 8 months ago
0
Automate monthly reports

#130 huddlej opened 8 months ago
0
Make Markdown output for reports

#129 huddlej closed 8 months ago
1
Update clades

#128 huddlej closed 9 months ago
0
Revisit deploy-private-nextflu Netlify CLI version pin

#127 joverlee521 opened 9 months ago
0
Fix deploy private

#126 joverlee521 closed 9 months ago
1