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modules lint: handle meta.ymls without topics field #3909

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Merged
mashehu merged 2 commits into from
Nov 18, 2025
Merged

modules lint: handle meta.ymls without topics field #3909

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e7485b0
modules lint: handle meta.ymls without topics field
mashehu Nov 18, 2025
1543e09
[automated] Update CHANGELOG.md
nf-core-bot Nov 18, 2025
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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 @@ -49,6 +49,7 @@

- Add `topics` to the template + update linting ([#3779](https://github.com/nf-core/tools/pull/3779))
- Preserve the value of self.modules_repo across nested calls ([#3881](https://github.com/nf-core/tools/pull/3881))
- modules lint: handle meta.ymls without topics field ([#3909](https://github.com/nf-core/tools/pull/3909))

### Subworkflows

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4 changes: 3 additions & 1 deletion nf_core/modules/lint/__init__.py
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Expand Up @@ -303,6 +303,7 @@ def update_meta_yml_file(self, mod):
if "output" in meta_yml:
correct_outputs = self.obtain_outputs(mod.outputs)
meta_outputs = self.obtain_outputs(meta_yml["output"])
if "topics" in meta_yml:
correct_topics = self.obtain_topics(mod.topics)
meta_topics = self.obtain_topics(meta_yml["topics"])

Expand Down Expand Up @@ -370,7 +371,8 @@ def _find_meta_info(meta_yml, element_name, is_output=False) -> dict:
corrected_meta_yml["output"][ch_name][i][element_name] = _find_meta_info(
meta_yml["output"], element_name, is_output=True
)
elif "topics" in meta_yml and correct_topics != meta_topics:

if "topics" in meta_yml and correct_topics != meta_topics:
log.debug(
f"Correct topics: '{correct_topics}' differ from current topics: '{meta_topics}' in '{mod.meta_yml}'"
)
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