Fetch and ingest #254

	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 4pm UTC (12pm EDT) since curation by NCBI happens on the East Coast.
	- cron: '0 16 * * 2'

	repository_dispatch:
	types:
	- fetch-and-ingest

	# Manually triggered using GitHub's UI
	workflow_dispatch:
	inputs:
	trial_name:
	description: 'Short name for a trial run. WARNING: without this we will overwrite files in s3://nextstrain-data/files/workflows/rsv'

	jobs:
	fetch-and-ingest:
	permissions:
	id-token: write
	uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
	secrets: inherit
	with:
	runtime: docker
	env: \|
	TRIAL_NAME: ${{ inputs.trial_name }}
	run: \|
	declare -a config

	if [[ "$TRIAL_NAME" ]]; then
	config+=("s3_dst=s3://nextstrain-data/files/workflows/rsv/trial/$TRIAL_NAME")
	fi

	nextstrain build \
	--env S3_DST \
	ingest \
	upload_all \
	--configfiles build-configs/nextstrain-automation/config.yaml \
	--config "${config[@]}"

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