Implement all checks in lint.yml directly

.github/workflows/lint.yml

@@ -28,5 +28,29 @@ jobs:
         # Conda-incubator uses 'test' environment by default.
       - name: install requirements
         run: mamba install -n test cromwell miniwdl wdl-aid
-      - name: run linting
-        run: bash scripts/biowdl_lint.sh
+      - name: run womtool validate
+        run: |
+          bash -c '
+            for WDL_FILE in $(git ls-files *.wdl); do
+              womtool validate $WDL_FILE
+            done
+          '
+      - name: run miniwdl check
+        run: bash -c 'miniwdl check $(git ls-files *.wdl)'
+      - name: Check copyright headers
+        run: | 
+          bash -c '
+            for WDL_FILE in $(git ls-files *.wdl); do
+              grep Copyright $WDL_FILE || bash -c "echo No copyright header in $WDL_FILE && exit 1"
+            done
+          '
+      - name: Check parameter_meta for inputs
+        run: |
+          bash -c '
+            for WDL_FILE in $(git ls-files *.wdl); do
+              wdl-aid --strict $WDL_FILE > /dev/null 2> wdl-aid_stderr || 
+              if grep -vz  "ValueError: Missing parameter_meta for inputs:" wdl-aid_stderr
+              then
+                 exit 1
+              fi
+          '