[Augur] Expose Augur versions #1987
Workflow file for this run
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@v4 | |
| # Select workflows with changes | |
| - uses: dorny/paths-filter@v3 | |
| 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"] | |
| #exclude: | |
| # - tag: "wf_theiacov_illumina_pe" | |
| # engine: "miniwdl" | |
| # - tag: "wf_theiacov_illumina_se" | |
| # engine: "miniwdl" | |
| defaults: | |
| run: | |
| # Play nicely with miniconda | |
| shell: bash -l {0} | |
| steps: | |
| # Checkout the repo | |
| - name: Checkout theiagen/public_health_bioinformatics | |
| uses: actions/checkout@v4 | |
| # Import test data | |
| - name: Pull Test Data from bactopia/bactopia-tests | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: bactopia/bactopia-tests | |
| path: bactopia-tests | |
| # # Setup Miniconda3 | |
| # - name: Setup miniconda | |
| # uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # activate-environment: actions | |
| # auto-activate-base: false | |
| # attempting micromamba install instead of miniconda3 in order to save on disk space | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: tests/config/environment.yml | |
| # # Depends and env info (mostly for debug) | |
| # # rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930 | |
| # - name: Install Dependencies and create storage space | |
| # run: | | |
| # conda install -y -c conda-forge -c bioconda cromwell miniwdl=1.5.2 'python>=3.7' pytest pytest-workflow 'importlib-metadata<=4.13.0' | |
| # conda clean -a -y | |
| # uname -a && env | |
| # sudo rm -rf /usr/share/dotnet | |
| # sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| # env info (mostly for debug) | |
| # rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930 | |
| - name: Env info and create storage space | |
| run: | | |
| micromamba list | |
| micromamba clean -a -y | |
| uname -a && env | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| sudo rm -rf /usr/local/lib/android | |
| df -h | |
| - name: Test ${{ matrix.tag }} | |
| run: TMPDIR=~ pytest --tag ${{ matrix.tag }}_${{ matrix.engine }} --symlink --kwdof --color=yes | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| 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_*/**/DATE | |
| /home/runner/pytest_workflow_*/**/VERSION | |
| !/home/runner/pytest_workflow_*/**/*.bam* | |
| !/home/runner/pytest_workflow_*/**/*.fastq.gz |