From 5b42b7596022ef91a1e2a01a32150243bccf4b29 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 26 Mar 2024 12:43:37 -0700 Subject: [PATCH] ingest-to-phylogenetic: Add phylogenetic job The phylogenetic workflow will run after the ingest workflow has completed successfully to use the latest available data. Subsequent commits will check if the ingest results included new data to only run the phylogenetic workflow when there's new data. --- .github/workflows/ingest-to-phylogenetic.yaml | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) 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/