GISAID fetch and ingest #1519
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| name: GISAID 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://gh.neting.ccmunity/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 GenBank 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 gisaid/fetch-and-ingest` | |
| repository_dispatch: | |
| types: | |
| - gisaid/fetch-and-ingest | |
| - fetch-and-ingest | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| inputs: | |
| trial_name: | |
| description: >- | |
| Short name for a trial run. | |
| If provided, files will be uploaded to s3://nextstrain-ncov-private/trial/${TRIAL_NAME}/ | |
| and downstream ncov and forecasts-ncov workflows will not be triggered. | |
| WARNING: without the trial name, workflow will upload files to s3://nextstrain-ncov-private/ | |
| required: false | |
| fetch_from_database: | |
| description: >- | |
| Whether the workflow should fetch from upstream database. | |
| If not selected (false), the workflow will start from existing data on S3. | |
| type: boolean | |
| required: false | |
| default: true | |
| image: | |
| description: >- | |
| Specific container image to use for build. | |
| This will override the default image (nextstrain/ncov-ingest). | |
| required: false | |
| jobs: | |
| set_config_overrides: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: config | |
| name: Set config overrides | |
| env: | |
| TRIAL_NAME: ${{ inputs.trial_name }} | |
| FETCH_FROM_DATABASE: ${{ github.event_name != 'workflow_dispatch' && true || inputs.fetch_from_database }} | |
| run: | | |
| config="--config" | |
| if [[ "$FETCH_FROM_DATABASE" == true ]]; then | |
| config+=" fetch_from_database=True" | |
| else | |
| config+=" fetch_from_database=False" | |
| fi | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+=" trigger_rebuild=False" | |
| config+=" trigger_counts=False" | |
| config+=" s3_dst=s3://nextstrain-ncov-private/trial/${TRIAL_NAME}" | |
| else | |
| config+=" trigger_rebuild=True" | |
| config+=" trigger_counts=True" | |
| fi | |
| echo "config=$config" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| config_overrides: ${{ steps.config.outputs.config }} | |
| fetch_and_ingest: | |
| needs: [set_config_overrides] | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| env: | | |
| CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }} | |
| GITHUB_RUN_ID: ${{ github.run_id }} | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image || 'nextstrain/ncov-ingest' }} | |
| SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || 'ncov-gisaid-updates' }} | |
| run: | | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 48 \ | |
| --memory 90GiB \ | |
| --env GISAID_API_ENDPOINT \ | |
| --env GISAID_USERNAME_AND_PASSWORD \ | |
| --env GITHUB_RUN_ID \ | |
| --env SLACK_TOKEN \ | |
| --env SLACK_CHANNELS \ | |
| --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \ | |
| . \ | |
| --stats snakemake_stats.json \ | |
| --configfile config/gisaid.yaml \ | |
| $CONFIG_OVERRIDES |