`modules update` with `patch` deletes files in `templates`
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bug
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
I customised the multiqc module to have a templates folder.
I then applied nf-core modules patch which generates a diff file for the main.nf
If I then run nf-core modules update multiqc the templates folder is removed.
Command used and terminal output
1. Add templates folder to module
2. nf-core modules patch
3. nf-core modules update multiqc
4. "Preview diff in terminal, choose whether to update files":
INFO 'modules/nf-core/multiqc/tests/tags.yml' is unchanged
INFO 'modules/nf-core/multiqc/templates/custom.ipynb' was removed
INFO 'modules/nf-core/multiqc/templates/custom_multiqc.py' was removed
System information
nf-core/tools version 2.14.2.dev0
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the reported sequence with nf-core modules patch followed by nf-core modules update multiqc, using the issue's terminal output as the expected failure. Trace the module patch and update handling for custom templates files; done means updating the module preserves that folder and its files.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100