Test with Nextflow from source #103
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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@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 | |
| with: | |
| repository: nextflow-io/nextflow | |
| path: nextflow | |
| - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 | |
| name: Check out nf-core/tools | |
| with: | |
| ref: dev | |
| path: nf-core-tools | |
| - name: Set up Python | |
| uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 | |
| with: | |
| python-version: "3.14" | |
| cache: pip | |
| cache-dependency-path: nf-core-tools/pyproject.toml | |
| - name: Set up Java | |
| uses: actions/setup-java@dded0888837ed1f317902acf8a20df0ad188d165 # v5 | |
| with: | |
| distribution: "temurin" | |
| architecture: x64 | |
| cache: 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 | |
| - name: Install nf-core/tools | |
| run: | | |
| cd nf-core-tools | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: Create new pipeline | |
| 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@v1 | |
| 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: ${{ secrets.NEXTFLOW_NIGHTLY_NOTIFICATION_EMAIL_ADDRESS }} | |
| from: [email protected] | |
| subject: "Nextflow source test CI failed" | |
| body: | | |
| The Nextflow source test CI workflow failed! | |
| See the failed run here: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} |