Merge branch 'main' into conditional-test

.github/workflows/cromwell-test-run.yml

@@ -44,11 +44,13 @@ jobs:
 
       - name: Execute Test Run of WDL Workflows
         run: |
-          java -jar cromwell-86.jar run helloHostname/helloHostname.wdl
-          java -jar cromwell-86.jar run helloModuleHostname/helloModuleHostname.wdl
-          java -jar cromwell-86.jar run helloDockerHostname/helloDockerHostname.wdl
-          java -jar cromwell-86.jar run conditionalTest/conditionalTest.wdl -i conditionalTest/inputs.json -o conditionalTest/options.json
-
-
-
+          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"
 

.github/workflows/womtools-validate.yml

@@ -47,10 +47,9 @@ jobs:
       - 
         name: Validate WDL Scripts
         run: |
-          java -jar womtool-86.jar validate helloHostname/helloHostname.wdl
-          java -jar womtool-86.jar validate helloModuleHostname/helloModuleHostname.wdl
-          java -jar womtool-86.jar validate helloDockerHostname/helloDockerHostname.wdl
-          java -jar womtool-86.jar validate conditionalTest/conditionalTest.wdl -i conditionalTest/inputs.json
-
-
-
+          cmd="java -jar womtool-86.jar validate ${{ matrix.wdl }}/${{ matrix.wdl }}.wdl"
+          if [[ -f "${{ matrix.wdl }}/inputs.json" ]]; then
+            cmd="$cmd -i ${{ matrix.wdl }}/inputs.json"
+          fi
+          echo "Running command: $cmd"
+          eval "$cmd"