diff --git a/.github/workflows/ingest-to-phylogenetic.yaml b/.github/workflows/ingest-to-phylogenetic.yaml index f55d4bb..602edc0 100644 --- a/.github/workflows/ingest-to-phylogenetic.yaml +++ b/.github/workflows/ingest-to-phylogenetic.yaml @@ -29,3 +29,34 @@ jobs: ingest/benchmarks/ ingest/logs/ ingest/.snakemake/log/ + + # TKTK check if ingest results include new data + # potentially use actions/cache to store Metadata.sha256sum of S3 files + + phylogenetic: + needs: [ingest] + permissions: + id-token: write + uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master + secrets: inherit + with: + # Starting with the default docker runtime + # We can migrate to AWS Batch when/if we need to for more resources or if + # the job runs longer than the GH Action limit of 6 hours. + runtime: docker + run: | + nextstrain build \ + --env AWS_ACCESS_KEY_ID \ + --env AWS_SECRET_ACCESS_KEY \ + phylogenetic \ + deploy_all \ + --configfile build-configs/nextstrain-automation/config.yaml + # Specifying artifact name to differentiate ingest build outputs from + # the phylogenetic build outputs + artifact-name: phylogenetic-build-output + artifact-paths: | + phylogenetic/auspice/ + phylogenetic/results/ + phylogenetic/benchmarks/ + phylogenetic/logs/ + phylogenetic/.snakemake/log/