I have a uv venv in my pipelines for running nf-core directly there. Note that this generates a .venv folder with all the packages when you run uv run sync.
I have the nextflow extension installed in vs code (1.6.1). The issue that I keep having is that the parsing? of the extension also reaches the .venv directory and starts complaining. The thing is that there is no real nextflow code in there.
If you click on the cog (settings) of the Nextflow extension, the 5th item down should be Nextflow > Files: Exclude. There should already be three items there, .git, .nf-test, and work. I also add my .pixi folder there too. So click the “Add item” and put .venv there.