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fix missing output files in test.yaml #1570

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merged 3 commits into from
May 12, 2022
Merged

fix missing output files in test.yaml #1570

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200b923
follow links when obtaining test output files
mirpedrol May 12, 2022
54c7b94
update CHANGELOG
mirpedrol May 12, 2022
e9be065
Merge branch 'dev' into missing_testfiles
mirpedrol May 12, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
- 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]
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2 changes: 1 addition & 1 deletion nf_core/modules/test_yml_builder.py
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Expand Up @@ -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":
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