Phylogenetic #2
Workflow file for this run
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| name: Phylogenetic | |
| defaults: | |
| run: | |
| # This is the same as GitHub Action's `bash` keyword as of 20 June 2023: | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell | |
| # | |
| # Completely spelling it out here so that GitHub can't change it out from under us | |
| # and we don't have to refer to the docs to know the expected behavior. | |
| shell: bash --noprofile --norc -eo pipefail {0} | |
| on: | |
| workflow_call: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| jobs: | |
| phylogenetic: | |
| 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 | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
| 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/ |