Backup nf-core pipelines #11
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| 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" | |
| # Add permissions block here | |
| permissions: | |
| id-token: write | |
| contents: read | |
| 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: ${{fromJson(needs.get-pipelines.outputs.matrix)}} | |
| fail-fast: false | |
| steps: | |
| - name: Clone the nf-core/${{ matrix.pipeline }} repository | |
| run: git clone --mirror https://github.com/nf-core/${{ matrix.pipeline }}.git | |
| - name: Make a tarball | |
| id: make-tarball | |
| run: | | |
| TARBALL_FILENAME="${{ matrix.pipeline }}_$(date +%Y-%m-%d_%H-%M).tar.gz" | |
| tar czf $TARBALL_FILENAME ${{ matrix.pipeline }}.git | |
| echo "TARBALL_FILENAME=$TARBALL_FILENAME" >> $GITHUB_OUTPUT | |
| - name: setup aws cli | |
| uses: aws-actions/configure-aws-credentials@67fbcbb121271f7775d2e7715933280b06314838 # v1 | |
| with: | |
| role-to-assume: ${{ secrets.AWS_BACKUP_ROLE }} | |
| aws-region: eu-west-1 | |
| role-session-name: GithubActionsBackup | |
| audience: sts.amazonaws.com | |
| - name: Upload repository to S3 | |
| run: | | |
| aws s3 cp "${{ steps.make-tarball.outputs.TARBALL_FILENAME }}" "s3express://nf-core-repos-backup--euw1-az1--x-s3/${{ steps.make-tarball.outputs.TARBALL_FILENAME }}" | |