Test with Nextflow from source #165
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| name: Test with Nextflow from source | |
| on: | |
| workflow_dispatch: # Manual trigger | |
| schedule: | |
| # Run at 00:00 UTC on Monday, Wednesday, Friday (2:00 CEST) | |
| - cron: "0 0 * * 1,3,5" | |
| jobs: | |
| test-with-nextflow-source: | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_ANSI_LOG: false | |
| steps: | |
| - name: Check out Nextflow | |
| uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| repository: nextflow-io/nextflow | |
| path: nextflow | |
| - name: Set up Java | |
| uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5 | |
| with: | |
| distribution: "temurin" | |
| architecture: x64 | |
| cache: gradle | |
| cache-dependency-path: "nextflow/**/*.gradle*" | |
| java-version: "21" | |
| - name: Build Nextflow | |
| run: cd nextflow && make pack | |
| - name: Move Nextflow to local bin/ | |
| run: | | |
| mkdir -p $HOME/.local/bin/ | |
| mv nextflow/build/releases/nextflow*dist $HOME/.local/bin/nextflow | |
| chmod +x $HOME/.local/bin/nextflow | |
| nextflow -version | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| name: Check out nf-core/tools | |
| with: | |
| ref: dev | |
| # Set up nf-core/tools | |
| - name: Set up Python 3.14 | |
| uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 | |
| with: | |
| python-version: "3.14" | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 | |
| with: | |
| enable-cache: true | |
| - name: Install nf-core/tools | |
| run: uv sync | |
| - name: Create new pipeline | |
| run: uv run nf-core pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" | |
| - name: Run new pipeline | |
| run: nextflow run nf-core-testpipeline -profile docker,test --outdir ./results | |
| - name: Send email on failure | |
| if: failure() | |
| uses: dsfx3d/action-aws-ses@a0daa3774d2bb09e2bcb512e55bdc3510b6102ef # v1.0.3 | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: "eu-west-1" | |
| with: | |
| to: ${{ secrets.NEXTFLOW_NIGHTLY_NOTIFICATION_EMAIL_ADDRESS }} | |
| from: core@nf-co.re | |
| subject: "Nextflow source test CI failed" | |
| body: | | |
| The Nextflow source test CI workflow failed! | |
| See the failed run here: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} |