Fetch and ingest #72
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: 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 4pm UTC (12pm EDT) since curation by NCBI happens on the East Coast. | |
| - cron: '0 16 * * 2' | |
| repository_dispatch: | |
| types: | |
| - fetch-and-ingest | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| jobs: | |
| fetch-and-ingest: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_RUN_ID: ${{ github.run_id }} | |
| SLACK_CHANNELS: rsv | |
| SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: nextstrain/.github/actions/setup-nextstrain-cli@master | |
| - name: run_pipeline | |
| run: | | |
| ./bin/write-envdir ingest/env.d \ | |
| AWS_DEFAULT_REGION \ | |
| GITHUB_RUN_ID \ | |
| SLACK_TOKEN \ | |
| SLACK_CHANNELS \ | |
| PAT_GITHUB_DISPATCH | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 8 \ | |
| --memory 32gib \ | |
| --exec env \ | |
| ingest \ | |
| envdir env.d snakemake \ | |
| --configfiles config/config.yaml config/optional.yaml \ | |
| --cores 8 \ | |
| --printshellcmds | |
| 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 }} | |
| PAT_GITHUB_DISPATCH: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }} | |
| - name: notify_pipeline_failed | |
| if: ${{ failure() }} | |
| run: ./ingest/bin/notify-on-job-fail |