Fetch and ingest #1977
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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 \ |