Merge pull request #1570 from mirpedrol/missing_testfiles

fix missing output files in test.yaml

CHANGELOG.md

@@ -28,6 +28,7 @@
 - Escaped test run output before logging it, to avoid a rich ` MarkupError`
 - Add a new command `nf-core modules mulled` which can generate the name for a multi-tool container image.
 - Add a new command `nf-core modules test` which runs pytests locally.
+- Allow follow links when generating `test.yml` file with `nf-core modules create-test-yml` ([1570](https://github.com/nf-core/tools/pull/1570))
 - Linting now recognised `shell` blocks to avoid error `when: condition has too many lines` ([#1557](https://github.com/nf-core/tools/issues/1557))
 
 ## [v2.3.2 - Mercury Vulture Fixed Formatting](https://github.com/nf-core/tools/releases/tag/2.3.2) - [2022-03-24]

nf_core/modules/test_yml_builder.py

@@ -225,7 +225,7 @@ 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, files in os.walk(results_dir):
+        for root, dir, files in os.walk(results_dir, followlinks=True):
             for filename in files:
                 # Check that the file is not versions.yml
                 if filename == "versions.yml":