move deploy workflow into workflows/ #1
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| name: Deploy Documentation | ||
| on: | ||
| workflow_call: | ||
| inputs: | ||
| deploy: | ||
| description: "Whether to deploy the website to GitHub Pages" | ||
| required: false | ||
| default: false | ||
| # Allow this job to clone the repo and create a page deployment | ||
| permissions: | ||
| contents: read | ||
| pages: write | ||
| id-token: write | ||
| concurrency: | ||
| group: "docs-deploy-${{ github.ref }}" | ||
| cancel-in-progress: true | ||
| jobs: | ||
| parameters-component: | ||
| name: pipeline_parameters | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| repository: scilus/nf-pediatric | ||
| ref: ${{ github.event.pull_request.head.sha || 'main' }} | ||
| path: nf-pediatric | ||
| fetch-depth: 0 # Shallow clones should be disabled for a version bump to work | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 | ||
| with: | ||
| python-version: "3.13" | ||
| architecture: "x64" | ||
| - name: read .nf-core.yml | ||
| uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 | ||
| id: read_yml | ||
| with: | ||
| config: ${{ github.workspace }}/.nf-core.yml | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | ||
| - name: Fetch pipeline parameters | ||
| id: pipeline_params | ||
| run: | | ||
| nf-core pipelines schema docs -o parameters.md -x markdown | ||
| echo '---' | cat - parameters.md > temp && mv temp parameters.md | ||
| echo 'title: Pipeline Parameters' | cat - parameters.md > temp && mv temp parameters.md | ||
| echo 'description: nf-pediatric parameters' | cat - parameters.md > temp && mv temp parameters.md | ||
| echo '---' | cat - parameters.md > temp && mv temp parameters.md | ||
| echo '' | cat - parameters.md > temp && mv temp parameters.md | ||
| - name: Pack into artifacts | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: markdown | ||
| path: parameters.md | ||
| build: | ||
| needs: parameters-component | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout website code | ||
| uses: actions/checkout@v4 | ||
| - name: Download pipeline parameters | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: markdown | ||
| path: src/content/docs/guides/ | ||
| - name: Install, build, and upload the site | ||
| uses: withastro/action@v2 | ||
| with: | ||
| node-version: 22 | ||
| package-manager: npm@latest | ||
| - name: Upload built site | ||
| uses: actions/upload-pages-artifact@v3 | ||
| with: | ||
| path: dist | ||
| deploy: | ||
| if: ${{ inputs.deploy == 'true' }} | ||
| needs: build | ||
| runs-on: ubuntu-latest | ||
| environment: | ||
| name: github-pages | ||
| url: ${{ steps.deployment.outputs.page_url }} | ||
| steps: | ||
| - name: Deploy to GitHub Pages | ||
| id: deployment | ||
| uses: actions/deploy-pages@v4 | ||
| preview-deploy: | ||
| if: ${{ inputs.deploy == 'false' && (github.event_name == 'pull_request' || github.event_name == 'pull_request_target') }} | ||
| needs: build | ||
| runs-on: ubuntu-latest | ||
| environment: | ||
| name: pr-preview-${{ github.event.pull_request.number }} | ||
| url: ${{ steps.preview.outputs.page_url }} | ||
| steps: | ||
| - name: Deploy PR preview to GitHub Pages | ||
| id: preview | ||
| uses: actions/deploy-pages@v4 | ||
| - name: Comment on PR with preview link | ||
| if: ${{ success() && (github.event_name == 'pull_request' || github.event_name == 'pull_request_target') }} | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| PREVIEW_URL: ${{ steps.preview.outputs.page_url }} | ||
| run: | | ||
| gh api repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments \ | ||
| -f body="🚀 **Documentation preview deployed!** | ||
| You can view the live preview here: | ||
| 👉 [${{ env.PREVIEW_URL }}](${{ env.PREVIEW_URL }}) | ||
| _(This preview will be automatically removed when the PR is closed or merged.)_" | ||
