update-sars-cov-2-datasets #10

	name: update-sars-cov-2-datasets

	on:
	schedule:
	# At 21:15 on Monday
	# https://crontab.guru/#15_21___1
	- cron: '15 21 * * 1'

	workflow_dispatch:

	repository_dispatch:
	types: update-sars-cov-2-datasets

	concurrency:
	group: update-sars-cov-2-datasets-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number \|\| github.ref \|\| github.run_id }}
	cancel-in-progress: true

	defaults:
	run:
	shell: bash -euxo pipefail {0}


	jobs:
	update-sars-cov-2-datasets:
	runs-on: ubuntu-24.04

	environment:
	name: ${{ github.ref }}

	steps:
	- name: "Checkout code"
	if: ${{ steps.config.outputs.is_fork != 'true' }}
	uses: actions/checkout@v4
	with:
	fetch-depth: 0 # Number of commits to fetch. 0 indicates all history for all branches and tags.
	fetch-tags: true # Whether to fetch tags, even if fetch-depth > 0.
	ref: ${{ github.head_ref \|\| github.ref }}

	- name: "Install dependencies"
	run: \|
	sudo apt-get install curl --yes -qq >/dev/null

	mkdir -p "${HOME}/bin"
	export PATH="${HOME}/bin:${PATH}"
	curl -fsSL "https://github.com/cli/cli/releases/download/v2.42.1/gh_2.42.1_linux_amd64.tar.gz" \| tar xz -C "${HOME}/bin" --strip-components=2 gh_2.42.1_linux_amd64/bin/gh

	- name: "Configure git"
	run: \|
	git config --global user.email "${{ secrets.BOT_GIT_USER_EMAIL }}"
	git config --global user.name "${{ secrets.BOT_GIT_USER_NAME }}"

	- name: "Update datasets"
	run: \|
	export GITHUB_TOKEN="${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_REPO }}"

	./scripts/update_sc2_datasets

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