Ingest to phylogenetic #28
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| name: Ingest to phylogenetic | |
| on: | |
| schedule: | |
| # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings. | |
| # | |
| # Currently, we aim to trigger runs at 7am UTC on Monday | |
| # | |
| # Note, '*' is a special character in YAML, so you have to quote this string. | |
| # | |
| # Docs: | |
| # - https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#schedule | |
| - cron: '0 7 * * 1' | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: >- | |
| Specific container image to use for build. | |
| This will override the default image (ghcr.io/nextstrain/tb:latest). | |
| required: false | |
| jobs: | |
| ingest_to_phylo: | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image || 'ghcr.io/nextstrain/tb:latest' }} | |
| run: | | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 72 \ | |
| --memory 140GiB \ | |
| . \ | |
| deploy_all \ | |
| --configfile build-configs/nextstrain-automation/config.yaml |