🚀 bcftools_markdup, bcftools_stats, fastqc, minimap2_align, picard_ma… #1
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| name: Test | |
| permissions: | |
| id-token: "write" | |
| contents: "write" | |
| packages: "write" | |
| pull-requests: "read" | |
| on: | |
| push: | |
| branches: | |
| - '**' | |
| paths: | |
| - '**/*.wdl' | |
| - 'tests/**.yaml' | |
| jobs: | |
| changed: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - run: sudo apt-get update && sudo apt-get install -y jq | |
| - name: Get changed file names | |
| id: set-matrix | |
| run: | | |
| changed_files_tags=$(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | sed -n '/^tasks\/.*\.wdl$/s|^tasks/||; s|\.wdl$||p') | |
| if [[ -z "$changed_files_tags" ]]; then | |
| echo "matrix=[]" >> $GITHUB_OUTPUT | |
| else | |
| matrix_json=$(echo "$changed_files_tags" | tr '\n' ' ' | jq -M -R -c 'split(" ") | map(select(. != ""))') | |
| echo $matrix_json | |
| echo "matrix=$matrix_json" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash -eo pipefail {0} | |
| test: | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.changed.outputs.matrix != '[]' }} | |
| needs: changed | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tag: ${{fromJson(needs.changed.outputs.matrix)}} | |
| services: | |
| docker: | |
| image: docker:19.03.12 | |
| options: --privileged | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| cache: 'pip' # caching pip dependencies | |
| - name: Install Python dependencies | |
| run: pip install -r tests/requirements.txt | |
| - name: Run test ${{ matrix.tag }} | |
| run: pytest --git-aware --tag ${{ matrix.tag }} --kwd --basetemp /tmp/ci tests/tasks | |
| - name: Prepare artifact name | |
| id: prepare_artifact_name | |
| run: | | |
| # This will replace slashes with dashes | |
| safe_artifact_name=$(echo "${{ matrix.tag }}" | sed 's:/:-:g') | |
| echo "safe_artifact_name=$safe_artifact_name" >> $GITHUB_ENV | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: ${{ env.safe_artifact_name }}-command | |
| path: | | |
| /tmp/ci/**/command | |
| /tmp/ci/**/*.err | |
| /tmp/ci/**/*.out |