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27 Open 43 Closed
27 Open 43 Closed
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Issues list

Annotate GISHN strains enhancement New feature or request
#196 opened Nov 12, 2024 by joverlee521
Update example GISAID workflow to support multiple input files enhancement New feature or request
#190 opened Oct 23, 2024 by huddlej
Update and standardize Nextclade datasets for all lineages and gene segments enhancement New feature or request
#186 opened Oct 15, 2024 by huddlej
@huddlej
Add GISAID isolate ID to acknowledgments download enhancement New feature or request
#178 opened Sep 5, 2024 by joverlee521
3 tasks done
1
4
Exclude sequences with unusual collection dates enhancement New feature or request
#175 opened Aug 6, 2024 by joverlee521
2
Rename master to main enhancement New feature or request
#169 opened Jun 11, 2024 by genehack
Use a narrative template file to stub out a date-specific narrative for a given set of dated builds
#163 opened May 13, 2024 by huddlej
Use metadata from NA segment in joined metadata when HA segment isn't available bug Something isn't working
#161 opened Apr 15, 2024 by huddlej
Automate deployment of private nextflu.org site enhancement New feature or request
#159 opened Apr 5, 2024 by joverlee521
"Suffolk" in lat_longs.tsv points to somewhere unexpected bug Something isn't working
#155 opened Feb 27, 2024 by fanninpm
1
1
Running issue nextstrain pipeline bug Something isn't working
#149 opened Feb 15, 2024 by sekhwal
18
Filter low-quality sequences by Nextclade QC status enhancement New feature or request
#144 opened Jan 30, 2024 by huddlej
Use Nextclade to assign clade labels in main phylogenetic workflow enhancement New feature or request
#131 opened Nov 28, 2023 by huddlej
Automate monthly reports enhancement New feature or request
#130 opened Nov 27, 2023 by huddlej
9 of 12 tasks
@huddlej @j23414
Revisit deploy-private-nextflu Netlify CLI version pin
#127 opened Nov 17, 2023 by joverlee521
Assign clades to nodes via tabular metadata enhancement New feature or request
#91 opened Nov 22, 2022 by uee9
Explore use of IQ-TREE's constraint tree option enhancement New feature or request
#79 opened Mar 23, 2022 by joverlee521
1
Minor typo in README: "depending on the assay that passage history of the antigens"? question Question about the project
#77 opened Jan 21, 2022 by corneliusroemer
Identify "prototype virus" for each putative clade enhancement New feature or request
#66 opened Aug 31, 2021 by huddlej
Annotate more granular clades on nextflu site enhancement New feature or request
#65 opened Aug 31, 2021 by huddlej
Divergence tree does not display properly on the x-axis for nextflu site bug Something isn't working
#61 opened Apr 20, 2021 by huddlej
@joverlee521
4
Some strain names in titer records are misspelled bug Something isn't working
#60 opened Apr 12, 2021 by huddlej
Refactor workflows to follow Nextstrain standards from ncov workflow enhancement New feature or request
#58 opened Dec 29, 2020 by huddlej
2 of 7 tasks
2
Estimate tip frequencies up to the month of latest available strains enhancement New feature or request
#54 opened Jul 14, 2020 by huddlej
Strains with ambiguous dates are assigned two different dates in auspice output bug Something isn't working
#48 opened Jan 10, 2020 by huddlej
@huddlej
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