Merge pull request #96 from uab-cgds-worthey/testing-detect-fix

adding testing detection function fix

Author: wilkb777

docs/Changelog.md

@@ -12,6 +12,10 @@ YYYY-MM-DD  John Doe
 ```
 ---
 
+2024-07-08  Brandon Wilk
+
+* Makes minor bug fix for issue #95 found in the test run detection logging function
+
 2023-10-09  Manavalan Gajapathy
 
 - Makes minor documentation updates - updating citation info, adding JOSS badge and updating zenodo badge to use generic

workflow/rules/common.smk

@@ -40,16 +40,23 @@ def is_testing_mode():
     "checks if testing dataset is used as input for the pipeline"
 
     query = ".test"
+    isTesting = False
     for sample in SAMPLES_CONFIG.values():
-        for fpath in sample.values():
-            if query in PurePath(fpath).parts:
-                logger.info(f"// WARNING: '{query}' present in at least one of the filepaths supplied via --sample_config. So testing mode is used.")
-                return True
+        for fvalue in sample.values():
+            if isinstance(fvalue, str) and query in PurePath(fvalue).parts:
+                isTesting = True
+            else:
+                for fpath in fvalue:
+                    if query in PurePath(fpath).parts:
+                        isTesting = True
+
+    if isTesting:
+        logger.info(f"// WARNING: '{query}' present in at least one of the filepaths supplied via --sample_config. So testing mode is used.")
+        return True
 
     return None
 
 
-
 def get_priorQC_filepaths(sample, samples_dict):
     """
     Returns filepaths relevant to priorQC