Backup nf-core pipelines #8

	name: Backup nf-core pipelines

	on:
	# schedule:
	# Runs at 00:00 UTC every Sunday
	# - cron: '0 0 * * 0' # TODO: Uncomment this after testing
	workflow_dispatch:
	inputs:
	pipeline:
	description: "Pipeline to backup"
	required: true
	default: "all"

	jobs:
	get-pipelines:
	runs-on: "ubuntu-latest"
	outputs:
	matrix: ${{ steps.set-matrix.outputs.matrix }}
	steps:
	- id: set-matrix
	run: \|
	json=$(curl -s https://nf-co.re/pipeline_names.json)
	# Default to "all" if running on schedule (no inputs available) or if input is "all"
	if [ -z "${{ inputs.pipeline }}" ] \|\| [ "${{ inputs.pipeline }}" = "all" ]; then
	echo "matrix=$(echo $json \| jq -c '.')" >> $GITHUB_OUTPUT
	else
	echo "matrix=$(echo $json \| jq -c --arg p "${{ inputs.pipeline }}" '{pipeline: [.pipeline[] \| select(. == $p)]}')" >> $GITHUB_OUTPUT
	fi

	backup:
	needs: get-pipelines
	runs-on: ubuntu-latest
	strategy:
	matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
	fail-fast: false

	env:
	TARBALL_FILENAME: ${{ matrix.pipeline }}_$(date +%Y-%m-%d_%H-%M).tar.gz

	steps:
	- name: Clone the repository
	run: git clone --mirror https://github.com/nf-core/${{ matrix.pipeline }}.git

	- name: Make a tarball
	run: tar czf $TARBALL_FILENAME ${{ matrix.pipeline }}.git

	- name: setup aws cli
	uses: aws-actions/configure-aws-credentials@67fbcbb121271f7775d2e7715933280b06314838 # v1
	with:
	role-to-assume: ${{ secrets.AWS_BACKUP_ROLE }}
	aws-region: eu-west-1

	- name: Upload repository to S3
	run: \|
	aws s3 cp $TARBALL_FILENAME s3express://nf-core-repos-backup--euw1-az1--x-s3/$TARBALL_FILENAME

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