diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml index 9548ab4c1a8..553a229549d 100644 --- a/.github/workflows/gatk-tests.yml +++ b/.github/workflows/gatk-tests.yml @@ -251,10 +251,10 @@ jobs: identifier: Java ${{ matrix.Java }} test on docker ${{matrix.testType}} only-artifact: ${{ needs.check-secrets.outputs.google-credentials != 'true' }} - #test wdl validation - wdlValidation: + #run wdl validation on WDLs in the scripts directory + scriptsWdlValidation: runs-on: ubuntu-latest - name: Validate WDLs using womtools + name: Validate scripts WDLs using womtools steps: - uses: actions/checkout@v2 with: @@ -262,13 +262,13 @@ jobs: - uses: ./.github/actions/install-cromwell with: CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }} - - name: Run WDL Validation Test - run: ./gradlew gatkWDLValidation + - name: Run Scripts WDL Validation Test + run: ./gradlew gatkValidateScriptsWdl - #test wdl auto generation - wdlGen: + #run wdl validation on generated WDLs + generatedWdlValidation: runs-on: ubuntu-latest - name: Test WDL Generation + name: Validate generated WDLs using womtools steps: - uses: actions/checkout@v2 with: @@ -283,8 +283,8 @@ jobs: with: CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }} - - name: Run WDL Generation Test - run: ./gradlew gatkWDLGenValidation + - name: Run Generated WDL Test + run: ./gradlew gatkValidateGeneratedWdl #Run our various targeted medium scale wdl wiring tests wdlTests: diff --git a/build.gradle b/build.gradle index 3d5ce51ddb4..8e991cd09ed 100644 --- a/build.gradle +++ b/build.gradle @@ -816,7 +816,7 @@ def execWDLValidation = { validateWDL -> } } -task gatkWDLValidation() { +task gatkValidateScriptsWdl() { doFirst { // running this task requires a local cromwell installation, with environment variables CROMWELL_JAR, // WOMTOOL_JAR set to the jar locations @@ -839,7 +839,7 @@ task gatkWDLValidation() { } } -task gatkWDLGenValidation(dependsOn: [gatkWDLGen, shadowJar]) { +task gatkValidateGeneratedWdl(dependsOn: [gatkWDLGen, shadowJar]) { doFirst { // running this task requires a local cromwell installation, with environment variables CROMWELL_JAR, // WOMTOOL_JAR set to the jar locations @@ -849,7 +849,7 @@ task gatkWDLGenValidation(dependsOn: [gatkWDLGen, shadowJar]) { } doLast { - // first, run the womtool validator + // first, run the womtool validator on WDL files in the 'doc/wdlGen' directory final File wdlGenFolder = new File("$docBuildDir/wdlGen") def wdlFiles = fileTree(dir: wdlGenFolder).filter { f -> !f.getAbsolutePath().endsWith(".html") && !f.getAbsolutePath().endsWith(".json")