I want to rewrite a decent nextflow pipeline into the nf-core framework, any advice/hints/short cuts? Seems like a good job for an LLM, which do folks recommend?

Just the framework right? It isn’t becoming an nf-core pipeline? Keep an eye on the branches available on github.com/nf-core/agents. I would start from an empty nf-core pipeline template (you said that up through the CLI, to have all the specs) and have LLM port all the pipeline logic itself to the empty pipeline.

Correct not becoming an nf-core pipeline but using the framework. Most local modules could be converted to nf-core modules

For converting modules, also have peek here. github.com/vagkaratzas/nf-core-module-dev

Open PRs back to the repo if you've optimized 😉

I am the repo owner 😭 essentially abandoned pipeline written by a rogue bioinformatician

I meant to Joon, PRs back to my bots xD