Refactor phylogenetic such that a reasonable phylogenetic/build-configs/ci works - Githubissues

nextstrain / WNV

the repository used to build West Nile Virus for nextstrain

https://nextstrain.org/WNV/NA

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Refactor phylogenetic such that a reasonable phylogenetic/build-configs/ci works #12

Closed j23414 closed 1 month ago

j23414 commented 2 months ago

Context

While adding https://github.com/nextstrain/pathogen-repo-guide/tree/main/phylogenetic/build-configs/ci realized phylogenetic was reading directly from ingest/results/ in https://github.com/nextstrain/WNV/blob/9c521cc783cecf610a5587ff0d2a3ffda8fa409f/phylogenetic/defaults/config.yaml#L9-L10

This may need to be refactored to work with our automation setup.

Description

[x] Add example sequences
[x] Instead of taking ingest/results/* as input, add a download or copy rule to prepare_sequences.smk
[x] Add phylogenetic/build-configs/ci check

Examples

Possible solution

(Optional)

j23414 commented 1 month ago

Closed since the last task was completed at https://github.com/nextstrain/WNV/commit/ec5dd338362ed1db4ac9b4a089acfbe6306db3d6