Validate test data in CI job

.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/[email protected]
+        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!"

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"
+}