How to set publishing mode for all processes?

[alnfedorov]

First, thank you guys for all the magnificent work! You made jobs of many bioinformaticians a lot easier.

I noticed that we no longer have a publish_dir_mode option available in this release(3.5). As far as I understand, it was removed in favor of setting this option for each particular process by selectors(#701).

Could you please provide an example of a Nextflow selector to reproduce the previous publish_dir_mode functionality?

I am far from being an expert in the Nextflow DSL, but wouldn't it require rewriting the whole publishDir definition?
I.e. publishDir.mode ='something' is not working. It should be publishDir = [path: ...., mode = 'something', ...]
(and the use case is to change only the mode parameter)

It might be worth mentioning a solution in the documentation.

[drpatelh]

Hi @alnfedorov ! Apologies for the late response!

I noticed that we no longer have a publish_dir_mode option available in this release(3.5). As far as I understand, it was removed in favor of setting this option for each particular process by selectors(#701).

Exactly! We thought it would be best to allow us to change this directly via a Nextflow config option rather than a custom params.publish_dir_mode option.

@mahesh-panchal do you have a solution we can use here? Might be nice to add an example of how we change the mode for a single process and for all via a config. I remember you mentioning that you had to define certain minimal components of publishDir together for the publishing to work properly e.g. path, mode etc.

[mahesh-panchal]

We should bring that parameter back:

nf-core/tools#1353 (comment)

I made a mistake when I thought I confirmed inheritance, but the test I made gave the result it did because of default settings.

[drpatelh]

This will be fixed in #770. I have added --publish_dir_mode back into the pipeline.