Fetch and ingest (on branch) #23

	name: Fetch and ingest (on branch)

	on:
	# 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

	env:
	NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }}

	jobs:
	fetch-and-ingest:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- uses: nextstrain/.github/actions/setup-nextstrain-cli@master
	with:
	cli-version: ">=7.1.0"
	python-version: "3.10"

	- name: install-pyyaml
	run: python3 -m pip install pyyaml

	- name: run_pipeline
	run: \|
	# Create JSON string for the nested upload config
	GITHUB_BRANCH=${GITHUB_REF#refs/heads/}
	S3_DST="s3://nextstrain-data/files/workflows/monkeypox/branch/${GITHUB_BRANCH}"
	UPLOAD_CONFIG=$(jq -n --arg S3_DST "$S3_DST" '{"s3": {"dst": $S3_DST }}')

	nextstrain build \
	--aws-batch \
	--detach \
	--no-download \
	--cpus 32 \
	--memory 64gib \
	--env AWS_DEFAULT_REGION \
	--env AWS_ACCESS_KEY_ID \
	--env AWS_SECRET_ACCESS_KEY \
	--env GITHUB_RUN_ID \
	ingest \
	--configfiles config/config.yaml config/optional.yaml \
	--config trigger_rebuild=False send_slack_notifications=False upload="$UPLOAD_CONFIG"
	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 }}
	GITHUB_RUN_ID: ${{ github.run_id }}

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