The ‘Maintainers Minutes’ aims to give further insight into the workings of the nf-core maintainers team by providing brief summaries of the monthly team meetings.
Overview
The last two maintainer meetings covered a wide range of topics from agentic-coding related topics to infrastructure updates, and of course, the usual discussions about the meaning of life.
Major topics covered in this period:
- Agentic coding and nf-core
- Configs strict syntax
- Deprecations documentation
- Topic migration progress
- Megatests snapshots
- Local modules in pipelines
- r-nf-core-utils
- Summer break and miscellaneous updates
Agentic coding and nf-core
RFC on agents
The agents.md and AI steering document RFC on agents has been accepted, and Igor is leading the effort. Next we will test the current approach in several pipelines, before adding a version of it to the pipelines template, and the modules repo.
Dealing with PRs made by/with agents
Related to that, we had a long discussion about how to deal with PRs made by or with agents. These were some of the several key points that were raised, and what we talked about:
- Snapshots hallucination: AI agents can sometimes generate incorrect content
- Human responsibility: The human launching agents should be responsible, not the reviewers
- Agent origin doesn’t matter: We don’t care if contributions come from an agent or a human, but the volume is concerning
- Closing unsatisfactory PRs: Maxime recommends just closing PRs if the reviewer is not happy
- Assisted by tags: It would be nice to have an “assisted by” comment or tag somewhere to identify AI-generated contributions
The general consensus was that an “assisted by” tag would be useful, and that in the end the human launching the agent should be responsible for the quality of the contribution. The reviewers should not be expected to verify the correctness of llm-generated content, and they are free to close PRs if they are not satisfied with the quality.
Configs strict syntax
The configs repository is almost fully following strict syntax and passing Nextflow linting. This is a major milestone for improving code quality and consistency across nf-core configurations.
Deprecations documentation
We need to reach a consensus on deprecation documentation. Related issues include:
The consensus is to create a failure assertion in the test. And we are assessing the modules deletion process a year after the deprecation. nf-core tools should handle this nicely, as the modules.json file might still be populated with the deprecated module.
Topic migration progress
End of May, the topic migration has reached the end of letter H, and covering 79%, showing steady progress. By the end of June, we are now at the letter M, which covers 88%, which shows the dedication of Louis into leading this herculean task. Note that since modules were not worked on alphabetically the letter is merely an indication as which modules we know have been covered for sure, and not a good measure.
Megatests snapshots
Maxime is hacking his way into megatests snapshots, working on improving nf-core’s testing infrastructure to better handle large-scale testing scenarios.
Local modules in pipelines
We discussed what to do with local modules in release PRs. The consensus was to:
- Document them in an issue
- Try to push as many as possible to the nf-core/modules repo
- Recommend using
modules patchwhen they diverge too much from the nf-core/modules repo
r-nf-core-utils
The r-nf-core-utils package has been approved, and released. This package will make writing R code for nf-core modules easier by providing helper functions for parsing Nextflow inputs and producing log/version files. A proof of concept is available at nf-core/modules#11933.
Containers in nf-core
tools dev has a new container subcommand
Tools dev has a new subcommand for migrating to seqera containers, nf-core modules container create.
It will facilitate automated container building and management.
Additionally, modules will get ARM compatibility on the side with this.
Meta pipelines
Meta pipelines are being discussed in nextflow-io/nextflow#7213.
Summer break
Summer break is coming, and both bytesizes and helpdesk will be on break. The maintainers meeting is also under evaluation.
End
That’s all folks! We’ll be back after the summer break with more updates and discussions.
- ❤️ from your #maintainers team!
