Merge pull request #1511 from asthara10/test_yml

CHANGELOG.md

@@ -33,6 +33,7 @@ Very minor patch release to fix the full size AWS tests and re-run the template
 - Remove traces of markdownlint in the template ([#1486](https://github.com/nf-core/tools/pull/1486)
 - Remove accidentally added line in `CHANGELOG.md` in the template ([#1487](https://github.com/nf-core/tools/pull/1487))
 - Update linting to check that `.editorconfig` is there and `.yamllint.yml` isn't.
+- Don't save md5sum for `versions.yml` when running `nf-core modules create-test-yml` ([#1511](https://github.com/nf-core/tools/pull/1511))
 
 ## [v2.3.1 - Mercury Vulture Formatting](https://github.com/nf-core/tools/releases/tag/2.3.1) - [2022-03-23]
 

nf_core/modules/test_yml_builder.py

@@ -225,21 +225,25 @@ def _md5(self, fname):
     def create_test_file_dict(self, results_dir, is_repeat=False):
         """Walk through directory and collect md5 sums"""
         test_files = []
-        for root, dir, file in os.walk(results_dir):
-            for elem in file:
-                elem = os.path.join(root, elem)
-                test_file = {"path": elem}  # add the key here so that it comes first in the dict
+        for root, dir, files in os.walk(results_dir):
+            for filename in files:
+                # Check that the file is not versions.yml
+                if filename == "versions.yml":
+                    continue
+                file_path = os.path.join(root, filename)
+                # add the key here so that it comes first in the dict
+                test_file = {"path": file_path}
                 # Check that this isn't an empty file
-                if self.check_if_empty_file(elem):
+                if self.check_if_empty_file(file_path):
                     if not is_repeat:
-                        self.errors.append(f"Empty file found! '{os.path.basename(elem)}'")
+                        self.errors.append(f"Empty file found! '{os.path.basename(file_path)}'")
                 # Add the md5 anyway, linting should fail later and can be manually removed if needed.
                 #  Originally we skipped this if empty, but then it's too easy to miss the warning.
                 #  Equally, if a file is legitimately empty we don't want to prevent this from working.
-                elem_md5 = self._md5(elem)
-                test_file["md5sum"] = elem_md5
+                file_md5 = self._md5(file_path)
+                test_file["md5sum"] = file_md5
                 # Switch out the results directory path with the expected 'output' directory
-                test_file["path"] = elem.replace(results_dir, "output")
+                test_file["path"] = file_path.replace(results_dir, "output")
                 test_files.append(test_file)
 
         test_files = sorted(test_files, key=operator.itemgetter("path"))