fix fuzzy_compile to get current branch and setup test_fuzzzy (#311)

Co-authored-by: Vasu Jaganath <vasu.jaganath@axleinfo.com>

.github/workflows/fuzzy_compile_weekly.yml

@@ -40,7 +40,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: ${{ github.repository_owner }}/sophios
-          ref: master
+          ref: ${{ inputs.wic_ref }}
           path: sophios
 
       - name: Checkout biobb_adapters
@@ -56,15 +56,15 @@ jobs:
         uses: actions/checkout@v3
         with:
           repository: ${{ github.repository_owner }}/mm-workflows
-          ref: main
+          ref: ${{ inputs.mm-workflows_ref }}
           path: mm-workflows
 
       - name: Checkout image-workflows
         if: always()
         uses: actions/checkout@v3
         with:
           repository: ${{ github.repository_owner }}/image-workflows
-          ref: main
+          ref: ${{ inputs.image-workflows_ref }}
           path: image-workflows
 
       - name: Setup miniforge (linux, macos)

src/sophios/utils.py

@@ -140,8 +140,12 @@ def get_steps_keys(steps: List[Yaml]) -> List[str]:
     Returns:
         List[str]: The name of each step in the given CWL workflow
     """
-    steps_keys = [step_dict['id'] for step_dict in steps]
-    # print(steps_keys)
+    steps_keys = []
+    for step_dict in steps:
+        if isinstance(step_dict, dict):
+            steps_keys.append(step_dict.get('id', ''))
+        else:
+            steps_keys.append('')
     return steps_keys
 
 
@@ -155,7 +159,7 @@ def get_subkeys(steps_keys: List[str]) -> List[str]:
     Returns:
         List[str]: The list of step keys associated with subworkflows of the current workflow.
     """
-    return [key for key in steps_keys if key.endswith('.wic')]
+    return [key for key in steps_keys if key and key.endswith('.wic')]
 
 
 def extract_implementation(yaml_tree: Yaml, wic: Yaml, yaml_path: Path) -> Tuple[str, Yaml]: