Generic pattern for multiple inputs for phylogenetic workflows added in https://github.com/nextstrain/pathogen-repo-guide/pull/91. [Updated 2026-02-19] ⭐ is a WA-DoH priority ([slack thread](https://bedfordlab.slack.com/archives/C01G4B4UY31/p1771456471584439)) ### TODOs - [x] https://github.com/nextstrain/avian-flu/pull/156 - [x] https://github.com/nextstrain/dengue/issues/114 - [ ] https://github.com/nextstrain/hmpv/issues/15 - [x] https://github.com/nextstrain/lassa/pull/77 - [x] https://github.com/nextstrain/measles/issues/82 - [x] ⭐ https://github.com/nextstrain/mpox/issues/324 - [x] https://github.com/nextstrain/mumps/pull/48 - [x] https://github.com/nextstrain/nipah/pull/17 - [x] ⭐ ncov - already using [standard config params](https://docs.nextstrain.org/projects/ncov/en/latest/reference/workflow-config-file.html#inputs) with additional functionality, probably best to just leave as-is - [x] https://github.com/nextstrain/norovirus/pull/34 - [ ] oropouche - [ ] rabies - [x] ⭐ https://github.com/nextstrain/rsv/issues/97 - [ ] rubella - [ ] seasonal-cov - [ ] ⭐ seasonal-flu - [x] ⭐ https://github.com/nextstrain/WNV/pull/110 - [ ] yellow-fever - [x] https://github.com/nextstrain/zika/pull/102
Generic pattern for multiple inputs for phylogenetic workflows added in nextstrain/pathogen-repo-guide#91.
[Updated 2026-02-19] ⭐ is a WA-DoH priority (slack thread)
TODOs