diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1a5e467..ce76452 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -6,7 +6,7 @@ on: branches: [ "master", "main" ] jobs: - build: + check_data_models: runs-on: ubuntu-latest strategy: matrix: @@ -38,3 +38,40 @@ jobs: run: | AnvilDataModels::json_to_dm("${{ matrix.data_model_file }}") shell: Rscript {0} + + check_test_data: + runs-on: ubuntu-latest + name: Check test data + steps: + + - name: Checkout repository + uses: actions/checkout@v3 + + - name: Checkout primed-file-checks + uses: actions/checkout@v3 + with: + repository: UW-GAC/primed-file-checks + path: primed-file-checks + + # Install Java to this VM. This Java version and distribution is compatible with Cromwell. + # This is the same step as used by broadinstitute/cromwell/.github/set_up_cromwell_action. + - name: Setup JDK + uses: actions/setup-java@v3 + with: + distribution: temurin + java-version: 11 + + # Get cromwell jar file + - uses: robinraju/release-downloader@v1.10 + with: + repository: 'broadinstitute/cromwell' + tag: '87' + fileName: 'cromwell-87.jar' + + - name: Validate test data + run: | + java -jar cromwell-87.jar run primed-file-checks/validate_phenotype_model.wdl --inputs test_data/wdl_inputs_validate_phenotype_model.json + shell: bash + + - name: Success! + run: echo "Success!" diff --git a/test_data/wdl_inputs_validate_phenotype_model.json b/test_data/wdl_inputs_validate_phenotype_model.json new file mode 100644 index 0000000..13653d5 --- /dev/null +++ b/test_data/wdl_inputs_validate_phenotype_model.json @@ -0,0 +1,11 @@ +{ + "validate_phenotype_model.table_files": { + "subject": "test_data/subject.tsv", + "phenotype_harmonized": "test_data/phenotype_harmonized.tsv" + }, + "validate_phenotype_model.model_url": "https://raw.githubusercontent.com/UW-GAC/primed-file-checks/main/testdata/data_model_phen.json", + "validate_phenotype_model.import_tables": false, + "validate_phenotype_model.overwrite": true, + "validate_phenotype_model.workspace_name": "PRIMED_pheno_QC_test", + "validate_phenotype_model.workspace_namespace": "primed-cc-scratch" +}