Looking at migrating a pipeline to the new workflow outputs and I am wondering: • what happens if multiple workflows declare a

publish

section? • does this mean I now have to manually bubble-up through nested subworkflows and publish every channel I care about?

or you can use topics

Wouldn't that require you to set those within each process? Not sure I fully grasp how this would work

iep

The best practice is to only publish in the entry workflow

Ooft yeah I think that topic setup is kind of messy personally, and I'm not a huge fan of patching modules. The benefit of the current publishDir style is that you don't have to choose what to publish until as late as runtime if you don't want to, which allows you to much more easily publish everything in dev/debug mode.

I think with records, good practice will be to bundle up e.g. sample-level output for a subworkflow into a single or handful of records, so you are only passing back a small number of more structured channels to publish

Yeah maybe I will just hold off until 26.04 and the record types come in then