Add GH Action for NCBI phylogenetic workflow #61
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This is a shared rule between the default builds and the full genome build and it works because both Snakemake workflows independently define their own `all` rule. As usual, this requires AWS credentials to upload the Auspice JSONs to the nextstrain-data S3 bucket.
Currently runs the full genome build and automatically uploads the resulting build to `s3://nextstrain-data`.
Allows us to test builds and deploy them to staging instead of production.
Will make edits in subsequent commit to reflect the default fauna build
I think the diff in this commit warrants maintaining separate GH Action workflows for NCBI vs fauna data builds instead of trying to shoehorn both into a single complicated GH Action workflow. Uses AWS Batch runtime with cpus/memory according to the repo's README instructions.¹ ¹ <https://github.com/nextstrain/avian-flu/blob/4ae5e32af0f00b3120d040bfd0b527a4b2c51c09/README.md?plain=1#L14>
genehack
approved these changes
Jun 21, 2024
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Description of proposed changes
Add GH Action workflows for the phylogenetic builds
The Phylogenetic NCBI workflow uses the public NCBI data for the full genome build and is able to run completely within the
dockerruntime on GH Actions.The Phylogenetic Fauna workflow uses the private fauna data for the default builds. I didn't check if it would complete within GH Actions and just followed the README instructions to run via
aws-batch.It's unclear how much manual curation is needed for NCBI ingest data before running builds so both need to be manually triggered for now.
Related issue(s)
Resolves #60
Checklist
https://nextstrain.org/staging/avian-flu/trials/gh-action-phylo/avian-flu/<subtype>/<segment>/<time>)