From 200b923267364def54d5c94ccf4a8b0e280bfaa0 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 12 May 2022 15:34:45 +0200 Subject: [PATCH 1/2] follow links when obtaining test output files --- nf_core/modules/test_yml_builder.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/modules/test_yml_builder.py b/nf_core/modules/test_yml_builder.py index fcdde14677..1739d52cb6 100644 --- a/nf_core/modules/test_yml_builder.py +++ b/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": From 54c7b9434bd428379f772007d846e66fe06bb527 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 12 May 2022 15:40:41 +0200 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95bba01f1b..4baf9257e2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ - 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)) ## [v2.3.2 - Mercury Vulture Fixed Formatting](https://github.com/nf-core/tools/releases/tag/2.3.2) - [2022-03-24]