diff --git a/.github/workflows/ingest-to-phylogenetic.yaml b/.github/workflows/ingest-to-phylogenetic.yaml new file mode 100644 index 0000000..0f6bc96 --- /dev/null +++ b/.github/workflows/ingest-to-phylogenetic.yaml @@ -0,0 +1,53 @@ +name: Ingest to phylogenetic + +on: + workflow_dispatch: + +jobs: + 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 \ + ingest \ + --configfile build-configs/nextstrain-automation/config.yaml + # Specifying artifact name to differentiate ingest build outputs from + # the phylogenetic build outputs + artifact-name: ingest-build-output + artifact-paths: | + ingest/results/ + ingest/benchmarks/ + ingest/logs/ + ingest/.snakemake/log/ + + # TKTK check for new data from ingest + # This can potentially interface with GH and/or S3? + # 1. Check last automated run's GH artifact output and diff with current S3 files + # 2. Check S3's previous version of outputs and diff with current S3 files + + # TKTK phylo workflow + # Just realized the phylo workflow does not have automated build uploads + + # phylogenetic: + # needs: [ingest] + # permissions: + # id-token: write + # uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master + # secrets: inherit + # with: + # runtime: docker + # run: | + # nextstrain build \ + # --env AWS_ACCESS_KEY_ID \ + # --env AWS_SECRET_ACCESS_KEY \ + # phylogenetic \ + # --configfile build-configs/nextstrain-automation/config.yaml