Fetch and ingest #2138
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| name: Fetch and ingest | |
| on: | |
| schedule: | |
| # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings. | |
| # | |
| # Note the actual runs might be late. | |
| # Numerous people were confused, about that, including me: | |
| # - https://github.community/t/scheduled-action-running-consistently-late/138025/11 | |
| # - https://github.com/github/docs/issues/3059 | |
| # | |
| # 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 | |
| # | |
| # Tool that deciphers this particular format of crontab string: | |
| # - https://crontab.guru/ | |
| # | |
| # Runs at 5pm UTC (1pm EDT/10am PDT) since curation by NCBI happens on the East Coast. | |
| # We were running into invalid zip archive errors at 9am PDT, so hoping an hour | |
| # delay will lower the error frequency | |
| - cron: '0 17 * * *' | |
| repository_dispatch: | |
| types: | |
| - fetch-and-ingest | |
| # 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 | |
| jobs: | |
| fetch-and-ingest: | |
| 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 }} | |
| GITHUB_RUN_ID: ${{ github.run_id }} | |
| SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }} | |
| run: | | |
| nextstrain build \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 32 \ | |
| --memory 64gib \ | |
| --env GITHUB_RUN_ID \ | |
| --env SLACK_TOKEN \ | |
| --env SLACK_CHANNELS \ | |
| --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \ | |
| ingest \ | |
| nextstrain_automation \ | |
| --configfiles build-configs/nextstrain-automation/config.yaml \ |