Fetch and ingest (on branch) #24

	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


	jobs:
	set_config_overrides:
	runs-on: ubuntu-latest
	steps:
	- id: upload_config
	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=$(jq -cn --arg S3_DST "$S3_DST" '{"s3": {"dst": $S3_DST }}')

	echo "upload_config=$UPLOAD_CONFIG" >> "$GITHUB_OUTPUT"
	outputs:
	upload_config: ${{ steps.upload_config.outputs.upload_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: \|
	NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
	GITHUB_RUN_ID: ${{ github.run_id }}
	UPLOAD_CONFIG: ${{ needs.set_config_overrides.outputs.upload_config }}
	run: \|
	nextstrain build \
	--aws-batch \
	--detach \
	--no-download \
	--cpus 32 \
	--memory 64gib \
	--env AWS_ACCESS_KEY_ID \
	--env AWS_SECRET_ACCESS_KEY \
	--env GITHUB_RUN_ID \
	ingest \
	--configfiles config/config.yaml config/optional.yaml \
	--config trigger_rebuild=False send_slack_notifications=False upload="$UPLOAD_CONFIG"

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