Update BenchmarkSVs workflow(s) with some new features #277
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
| name: WDL Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| schedule: | |
| - cron: '23 2 * * *' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| validate: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/actions/install-cromwell | |
| with: | |
| CROMWELL_VERSION: 87 | |
| - name: Womtool Validate | |
| run: find . -name '*.wdl' | xargs -tI {} java -jar ${WOMTOOL_JAR} validate {} | |
| test: | |
| needs: validate | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - id: auth | |
| name: 'Authenticate to Google Cloud' | |
| uses: 'google-github-actions/auth@v2' | |
| with: | |
| workload_identity_provider: 'projects/1038484894585/locations/global/workloadIdentityPools/github-wi-pool/providers/github-wi-provider' | |
| service_account: palantir-workflows-service-acc@broad-dsde-methods.iam.gserviceaccount.com | |
| - uses: ./.github/actions/install-cromwell | |
| with: | |
| CROMWELL_VERSION: 87 | |
| - uses: ./.github/actions/install-watt | |
| with: | |
| WATT_VERSION: v1.1 | |
| - name: Get changed Files | |
| if: github.ref != 'refs/heads/main' | |
| id: changed-files | |
| uses: tj-actions/changed-files@v44 | |
| with: | |
| files_yaml: | | |
| wdl: '**.wdl' | |
| json: '**.json' | |
| watt_config: test/watt_config.yml | |
| - name: Choose tests to run | |
| id: choose_tests_to_run | |
| if: github.ref != 'refs/heads/main' && !steps.changed-files.outputs.watt_config_all_changed_and_modified_files && (steps.changed-files.outputs.wdl_all_changed_and_modified_files || steps.changed-files.outputs.json_all_changed_and_modified_files) | |
| env: | |
| CHANGED_WDLS: ${{ steps.changed-files.outputs.wdl_all_changed_and_modified_files }} | |
| CHANGED_JSON: ${{ steps.changed-files.outputs.json_all_changed_and_modified_files }} | |
| run: | | |
| WF_TESTS_TO_RUN=$(python test/choose_watt_tests/choose_watt_tests.py --watt-config test/watt_config.yml --womtool-jar ${WOMTOOL_JAR} --changed-workflows ${CHANGED_WDLS} --changed-jsons ${CHANGED_JSON}) | |
| # remove white space elements from bash array | |
| for i in ${!WF_TESTS_TO_RUN[@]}; do [[ -z ${WF_TESTS_TO_RUN[i]} ]] && unset WF_TESTS_TO_RUN[i]; done | |
| if [[ ${#WF_TESTS_TO_RUN[@]} == 0 ]]; then | |
| echo "No workflows with tests have changed. Will not run any tests" | |
| else | |
| echo "Running tests for ${#WF_TESTS_TO_RUN[@]} workflows: ${WF_TESTS_TO_RUN}" | |
| echo "WF_TESTS_TO_RUN=${WF_TESTS_TO_RUN}" >> $GITHUB_ENV | |
| fi | |
| echo "n_wf_to_test=${#WF_TESTS_TO_RUN[@]}" >> $GITHUB_OUTPUT | |
| - name: Run tests with WATT | |
| if: steps.choose_tests_to_run.outputs.n_wf_to_test > 0 || github.ref == 'refs/heads/main' || steps.changed-files.outputs.watt_config_all_changed_and_modified_files | |
| env: | |
| WF_PARAM_NAME: ${{ steps.choose_tests_to_run.outputs.n_wf_to_test && '--workflow' || '' }} | |
| run: python ~/watt/watt.py -e ${CROMWELL_JAR} -c test/watt_config.yml ${WF_PARAM_NAME} ${WF_TESTS_TO_RUN} --cromwell-config test/simple_cromwell.conf -p 50 --executor-log-prefix cromwell_logs/ | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: cromwell_logs | |
| path: cromwell_logs/ |