Subject says it. Something about moving all of the publishing “out” to the workflow level feels very wrong from an information-hiding perspective. For standardization across our process library we rely on publishDir to effectively handle process-specific outputs. In many cases those outputs are written to S3 and aren’t interesting to the workflow itself. But, if I’m reading the description the right way we won’t be able to do that soon-ish?
You can read this guide for more explanation of why Nextflow is moving to workflow outputs.
To answer your immediate question, publishDir will be deprecated but likely won’t be removed for a while. It can be a significant shift, even though I think the benefits are worth it, so we don’t expect people to transition overnight.
The guide has more to say about it, but I will say this – even if a process output is not used downstream in your workflow, it is a “workflow-level” output because it is an effect of running your pipeline. So it is useful to have all of the published outputs modeled in one place at the top-level. This will also enable other functionality in the future like pipeline chaining.