Comments (2)
joverlee521
commented on July 19, 2024
1
Bumping this issue because we were asked during Nextstrain office hours (Oct 7, 2021) if we have plans to create a flu workflow similar to the ncov template/tutorial.
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huddlej
commented on July 19, 2024
Additional considerations:
- Do we want to rewrite the whole workflow from scratch or refactor the existing workflow?
- Should we continue to consider the WHO builds as a separate workflow or will we eventually be able to run those builds with the “live” workflow?
- Do we need to create separate trees for each combination of collaborating center and assay type or can we build a single tree and run the titer models multiple times for each combination of data with the same tree?
- Trees would need to prioritize strains based on all available titer measurements.
- How do we want to deploy "private" trees for collaborating centers?
- Private Nextstrain Groups seem like an obvious solution, but should we have one group per CC or a single group for all?
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Related Issues (20)
- Example build not working. MissingRuleException HOT 6
- Unable to run nextstrain command under 'Quickstart with GISAID data' HOT 3
- Revisit deploy-private-nextflu Netlify CLI version pin
- Automate monthly reports
- Use Nextclade to assign clade labels in main phylogenetic workflow
- Export GISAID accessions from metadata into Auspice JSONs
- Add rules to the nextflu-private workflow to rename Auspice JSONs based on the build date and deploy the JSONs to the Nextstrain group
- Filter low-quality sequences by Nextclade QC status
- Integrating FASTA Sequence into Influenza A/H3N2 Evolution Analysis and Visualizing in Nextclade HOT 6
- Running issue nextstrain pipeline HOT 18
- Rename public nextstrain builds to `seasonal-flu`
- "Suffolk" in `lat_longs.tsv` points to somewhere unexpected HOT 1
- Automate deployment of private nextflu.org site
- Use metadata from NA segment in joined metadata when HA segment isn't available
- Plot counts per lineage by region with matplotlib instead of altair
- Use a narrative template file to stub out a date-specific narrative for a given set of dated builds
- Use existing public 2y builds as “representative” trees in our reports
- Rename `master` to `main`
- Nextclade dataset for "broad" H1N1pdm HA misassigns early clade labels
- Run pathogen-embed on HA/NA alignments to flag putative reassortant clades
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