[Augur +TheiaCoV] Enable H5N1 flu subtype augur & nextclade #1690
Workflow file for this run
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| # | |
| # 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 |