♻️ Refactor logic in bulk RNA-seq use case #60
Workflow file for this run
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| name: build | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main, staging] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-22.04 | |
| env: | |
| GITHUB_EVENT_NAME: ${{ github.event_name }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9"] | |
| timeout-minutes: 50 | |
| steps: | |
| - name: Checkout main | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Checkout lndocs | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: laminlabs/lndocs | |
| ssh-key: ${{ secrets.READ_LNDOCS }} | |
| path: lndocs | |
| ref: main | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| cache-dependency-path: ".github/workflows/build.yml" # See dependencies below | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "latest-stable" | |
| - name: Cache Nextflow output | |
| uses: actions/cache@v2 | |
| with: | |
| path: docs/guide/nextflow_rna_seq/rna-seq-results | |
| key: ${{ runner.os }}-nextflow-rna-seq-results | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pre-commit | |
| key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }} | |
| - name: Cache postgres | |
| id: cache-postgres | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/postgres.tar | |
| key: cache-postgres-0 | |
| - name: Cache postgres miss | |
| if: steps.cache-postgres.outputs.cache-hit != 'true' | |
| run: docker pull postgres:latest && docker image save postgres:latest --output ~/postgres.tar | |
| - name: Cache postgres use | |
| if: steps.cache-postgres.outputs.cache-hit == 'true' | |
| run: docker image load --input ~/postgres.tar | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install -U pip | |
| pip install -U laminci | |
| - uses: aws-actions/configure-aws-credentials@v2 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: eu-central-1 | |
| - run: nox -s lint | |
| - run: nox -s build | |
| - uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - uses: nwtgck/[email protected] | |
| with: | |
| publish-dir: "_build/html" | |
| production-deploy: ${{ github.event_name == 'push' }} | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| enable-commit-comment: false | |
| env: | |
| NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} | |
| NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }} |