added cromwell tests docs in readme #20
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| name: Cromwell Test Run | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| generate-matrix: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Find WDL Directories | |
| id: set-matrix | |
| run: | | |
| # Find all directories containing .wdl files | |
| dirs=$(find . -type f -name "*.wdl" -exec dirname {} \; | sort -u | sed 's|^\./||' | jq -R . | jq -s | jq -c .) | |
| echo "Directories: $dirs" | |
| echo "matrix=$dirs" >> $GITHUB_OUTPUT | |
| testrun: | |
| needs: generate-matrix | |
| if: ${{ github.event.pull_request.head.repo.fork == false }} | |
| runs-on: ubuntu-latest | |
| permissions: write-all | |
| strategy: | |
| matrix: | |
| wdl: ${{ fromJson(needs.generate-matrix.outputs.matrix) }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set Up Java | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '21' | |
| - name: Pull Cromwell Jarfile | |
| run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/cromwell-86.jar | |
| - name: Execute Test Run of WDL Workflows | |
| run: | | |
| cmd="java -jar cromwell-86.jar run ${{ matrix.wdl }}/${{ matrix.wdl }}.wdl" | |
| if [[ -f "${{ matrix.wdl }}/inputs.json" ]]; then | |
| cmd="$cmd -i ${{ matrix.wdl }}/inputs.json" | |
| fi | |
| if [[ -f "${{ matrix.wdl }}/options.json" ]]; then | |
| cmd="$cmd -o ${{ matrix.wdl }}/options.json" | |
| fi | |
| echo "Running command: $cmd" | |
| eval "$cmd" | |