Skip to content

Fix wrong key when updating module outputs #3665

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Jul 8, 2025
Merged

Fix wrong key when updating module outputs #3665

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
6a4bd33
fix wrong key when updating module outputs
mirpedrol Jul 8, 2025
f1e6650
[automated] Update CHANGELOG.md
nf-core-bot Jul 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@

- Remove args stub from module template to satisfy language server ([#3403](https://github.com/nf-core/tools/pull/3403))
- Fix modules meta.yml file structure ([#3532](https://github.com/nf-core/tools/pull/3532))
- Fix wrong key when updating module outputs ([#3665](https://github.com/nf-core/tools/pull/3665))

### Subworkflows

Expand Down
22 changes: 11 additions & 11 deletions nf_core/modules/lint/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -324,7 +324,7 @@ def _find_meta_info(meta_yml, element_name, is_output=False) -> dict:
if isinstance(meta_channel, list):
for x, meta_element in enumerate(meta_channel):
if element_name == list(meta_element.keys())[0]:
return meta_yml[k][x][element_name]
return meta_yml[ch_name][k][x][element_name]
elif isinstance(meta_channel, dict):
if element_name == list(meta_channel.keys())[0]:
return meta_yml[ch_name][k][element_name]
Expand Down Expand Up @@ -356,18 +356,18 @@ def _find_meta_info(meta_yml, element_name, is_output=False) -> dict:
mod.outputs.copy()
) # eg. { bam: [[ {meta:{}}, {*.bam:{}} ]], reference: [ {*.fa:{}} ] } -> 2 channels, a tuple (list) and a single path (dict)
for ch_name in corrected_meta_yml["output"].keys():
ch_content = corrected_meta_yml["output"][ch_name][0]
if isinstance(ch_content, list):
for i, element in enumerate(ch_content):
element_name = list(element.keys())[0]
corrected_meta_yml["output"][ch_name][0][i][element_name] = _find_meta_info(
for i, ch_content in enumerate(corrected_meta_yml["output"][ch_name]):
if isinstance(ch_content, list):
for j, element in enumerate(ch_content):
element_name = list(element.keys())[0]
corrected_meta_yml["output"][ch_name][i][j][element_name] = _find_meta_info(
meta_yml["output"], element_name, is_output=True
)
elif isinstance(ch_content, dict):
element_name = list(ch_content.keys())[0]
corrected_meta_yml["output"][ch_name][i][element_name] = _find_meta_info(
meta_yml["output"], element_name, is_output=True
)
elif isinstance(ch_content, dict):
element_name = list(ch_content.keys())[0]
corrected_meta_yml["output"][ch_name][0][element_name] = _find_meta_info(
meta_yml["output"], element_name, is_output=True
)

def _add_edam_ontologies(section, edam_formats, desc):
expected_ontologies = []
Expand Down