Error linting module that has the keyword `val` in its emit name
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- Python
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Description
Description of the bug
I am linting the module reconst/shmetrics on my nf-core/modules clone (nf-neuro). I'm getting a lint error that the output section is badly formatted, saying the output peak_values should have this shape :
'peak_values': ['meta', '*peak_values.nii.gz', 'ues']
The last element (ues) should not be there. I am not well versed in regex, but I believe it gets extracted by the one that is here in the nf-core/tools code.
Command used and terminal output
git clone https://github.com/AlexVCaron/nf-neuro.git nf-neuro
cd nf-neuro
git checkout feat/nf-core_3.2.0
nf-core modules lint reconst/shmetrics
System information
- Nextflow 24.10.3
- Desktop
- local
- Ubuntu 22.04
- nf-core/tools 3.2.0
- Python 3.10.12
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First steps
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- Open a pull request that references the issue number.
Research direction
Reproduce the problem with nf-core modules lint reconst/shmetrics in the nf-neuro clone, then inspect nf_core/components/nfcore_component.py around line 249 and its output-name parsing. Confirm why ues is extracted from the peak_values emit name; done means the lint output accepts the module's output format without the spurious suffix.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100