Backup nf-core pipelines #5
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| name: Clone and Upload to S3 | |
| 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: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - id: set-matrix | |
| run: | | |
| matrix=$(curl https://nf-co.re/pipeline_names.json) | |
| # Extract the pipeline array from the JSON structure | |
| matrix=$(echo $matrix | jq '.pipeline') | |
| if [ -n "${{ inputs.pipeline }}" ] && [ "${{ inputs.pipeline }}" != "all" ]; then | |
| matrix=$(echo $matrix | jq --arg pipeline "${{ inputs.pipeline }}" '[.[] | select(. == $pipeline)]') | |
| fi | |
| echo "matrix=${matrix}" >> $GITHUB_OUTPUT | |
| 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@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 |