new module: ESTSFS #77
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Pytest-workflow | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| changes: | |
| name: Check for changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dorny/paths-filter@v3 | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| test: | |
| runs-on: ubuntu-latest | |
| name: ${{ matrix.tags }} ${{ matrix.profile }} | |
| needs: changes | |
| if: needs.changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| env: | |
| NXF_ANSI_LOG: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow | |
| - uses: actions/cache@v3 | |
| with: | |
| path: /usr/local/bin/nextflow | |
| key: ${{ runner.os }} | |
| restore-keys: | | |
| ${{ runner.os }}-nextflow- | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-singularity@v5 | |
| with: | |
| singularity-version: 3.7.1 | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda clean | |
| if: matrix.profile == 'conda' | |
| run: conda clean -a | |
| # Test the module | |
| - name: Run pytest-workflow | |
| # only use one thread for pytest-workflow to avoid race condition on conda cache. | |
| run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs-${{ matrix.profile }} | |
| path: | | |
| /home/runner/pytest_workflow_*/*/.nextflow.log | |
| /home/runner/pytest_workflow_*/*/log.out | |
| /home/runner/pytest_workflow_*/*/log.err | |
| /home/runner/pytest_workflow_*/*/work | |
| !/home/runner/pytest_workflow_*/*/work/conda | |
| !/home/runner/pytest_workflow_*/*/work/singularity |