GenBank fetch and ingest #786
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| name: GenBank fetch and ingest | |
| on: | |
| schedule: | |
| # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings. | |
| # | |
| # Currently, we aim to trigger ingest every day at 18:07 UTC which is 19:07 CET (as of Mar 2022). | |
| # Note the actual runs might be late. As of right now, the action starts around 20 past the hour. | |
| # Numerous people were confused, about that, including me: | |
| # - https://git.luolix.topmunity/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/ | |
| # | |
| # Looks like you are about to modify this schedule? Make sure you also modify the schedule for the | |
| # sister GISAID job, so that we don't need to keep two schedules in our heads. | |
| - cron: '7 18 * * *' | |
| # Manually triggered using `./vendored/trigger nextstrain/ncov-ingest genbank/fetch-and-ingest` (or `fetch-and-ingest`, which | |
| # includes GISAID) | |
| repository_dispatch: | |
| types: | |
| - genbank/fetch-and-ingest | |
| - 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: ncov-genbank-updates | |
| SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: nextstrain/.github/actions/setup-nextstrain-cli@master | |
| - name: run_pipeline | |
| run: | | |
| ./bin/write-envdir env.d \ | |
| AWS_DEFAULT_REGION \ | |
| GITHUB_RUN_ID \ | |
| SLACK_TOKEN \ | |
| SLACK_CHANNELS \ | |
| PAT_GITHUB_DISPATCH | |
| declare -a config | |
| config+=( | |
| fetch_from_database=True | |
| trigger_rebuild=True | |
| trigger_counts=True | |
| ) | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --image nextstrain/ncov-ingest \ | |
| --cpus 16 \ | |
| --memory 68GiB \ | |
| --exec env \ | |
| . \ | |
| envdir env.d snakemake \ | |
| --configfile config/genbank.yaml \ | |
| --config "${config[@]}" \ | |
| --cores 16 \ | |
| --resources mem_mb=68000 \ | |
| --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: ./vendored/notify-on-job-fail Ingest nextstrain/ncov-ingest |