update readme (#224) #173
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
| # | |
| # This workflow will run on Pushes and Pull Requests against the main branch. It | |
| # will run pytest with MiniWDL and Cromwell for any workflows with a change to | |
| # them or associated tasks. | |
| # | |
| name: Pytest Workflows | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| changes: | |
| name: Check for changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose workflows with changes | |
| workflows: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| # Checkout the repo | |
| - uses: actions/checkout@v3 | |
| # Select workflows with changes | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_filter.yml" | |
| check: | |
| runs-on: ubuntu-20.04 | |
| name: ${{ matrix.tag }} ${{ matrix.engine }} | |
| needs: changes | |
| if: ${{ needs.changes.outputs.workflows != '[]' && needs.changes.outputs.workflows != '' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # For every workflow, test it with MiniWDL and Cromwell | |
| tag: ["${{ fromJson(needs.changes.outputs.workflows) }}"] | |
| engine: ["miniwdl", "cromwell"] | |
| defaults: | |
| run: | |
| # Play nicely with miniconda | |
| shell: bash -l {0} | |
| steps: | |
| # Checkout the repo | |
| - name: Checkout theiagen/public_health_viral_genomics | |
| uses: actions/checkout@v3 | |
| # Setup Miniconda3 | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: actions | |
| auto-activate-base: false | |
| # Install dependencies; clean up conda garbage; and print env info (mostly for debug) | |
| # rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930 | |
| - name: Install Dependencies | |
| run: | | |
| conda install -y -c conda-forge -c bioconda cromwell miniwdl 'python>=3.7' pytest pytest-workflow | |
| conda clean -a -y | |
| uname -a && env | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Test ${{ matrix.tag }} | |
| run: TMPDIR=~ pytest --tag ${{ matrix.tag }}_${{ matrix.engine }} --symlink --kwdof --color=yes --git-aware | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs-${{ matrix.engine }} | |
| path: | | |
| /home/runner/pytest_workflow_*/**/stdout* | |
| /home/runner/pytest_workflow_*/**/stderr* | |
| /home/runner/pytest_workflow_*/**/script* | |
| /home/runner/pytest_workflow_*/**/rc | |
| /home/runner/pytest_workflow_*/**/command | |
| /home/runner/pytest_workflow_*/**/*.txt | |
| /home/runner/pytest_workflow_*/**/*.log | |
| /home/runner/pytest_workflow_*/**/*.out | |
| /home/runner/pytest_workflow_*/**/*.err | |
| /home/runner/pytest_workflow_*/**/*.json | |
| /home/runner/pytest_workflow_*/**/DATE | |
| /home/runner/pytest_workflow_*/**/VERSION | |
| !/home/runner/pytest_workflow_*/**/*.bam* | |
| !/home/runner/pytest_workflow_*/**/*.fastq.gz |