Ingest to phylogenetic #4
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 \ | |
| upload_all \ | |
| --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 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: | |
| 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 |