Fetch and ingest (on branch) #19
Workflow file for this run
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| name: Fetch and ingest (on branch) | |
| on: | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for build (will override the default of "nextstrain build")' | |
| required: false | |
| env: | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }} | |
| jobs: | |
| fetch-and-ingest: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: nextstrain/.github/actions/setup-nextstrain-cli@master | |
| with: | |
| cli-version: ">=7.1.0" | |
| python-version: "3.10" | |
| - name: install-pyyaml | |
| run: python3 -m pip install pyyaml | |
| - name: run_pipeline | |
| run: | | |
| GITHUB_BRANCH=${GITHUB_REF#refs/heads/} | |
| ./phylogenetic/bin/set-branch-ingest-config \ | |
| --config-yaml ingest/config/optional.yaml \ | |
| --s3-dst s3://nextstrain-data/files/workflows/monkeypox/branch/"${GITHUB_BRANCH}" \ | |
| > ingest/config/optional-branch.yaml | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 32 \ | |
| --memory 64gib \ | |
| --env AWS_DEFAULT_REGION \ | |
| --env AWS_ACCESS_KEY_ID \ | |
| --env AWS_SECRET_ACCESS_KEY \ | |
| --env GITHUB_RUN_ID \ | |
| ingest \ | |
| --configfiles config/config.yaml config/optional-branch.yaml \ | |
| --config trigger_rebuild=False | |
| env: | |
| AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| GITHUB_RUN_ID: ${{ github.run_id }} |