Handling with patched modules in subworkflows
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enhancement
infrastructure
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of feature
As discussing with @mashehu during the nf-core hackathon, we need to deal with patched modules used in subworkflows.
TODOs:
- When installing a subworkflow with
nf-core subworkflows installif there's a module needed in the subworkflow and already installed, it asks the user to force re-install the module. Currently, it deletes the module folder and installs it fresh. We need to check if that module has a patch file to save it and apply after the installation. - When a module is patched, throw a warning telling the user that this might break the subworkflow.
- When a module is patched, offer the option to run tests. Pull tests from the
nf-core/modulesrepo if it's available and run them.
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
Start by tracing the nf-core subworkflows install entry point and how patched modules are represented. Review the interaction with the nf-core/modules repository and define how installation preserves and reapplies patches, warns about subworkflow breakage, and optionally runs available module tests. Done means all three TODOs are covered.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100