add runOptions to Docker profile to fix ownership on files

[maxulysse]

Add runOptions to Docker profile to fix ownership on files.
Otherwise we have Permission denied when deleting the work directory.

[apeltzer]

Looks good :) Nice!

[ewels]

This makes me a little nervous. Will it have any off-target affects?

@pditommaso - why is this not the default in Nextflow?

[maxulysse]

There was also the fixOwnership setting in the Docker scope

[ewels]

There was also the fixOwnership setting in the Docker scope

Does this have the same effect? I'm a bit scared of changing these kinds of defaults in case it breaks everything for people running say, kubernetes.

[maxulysse]

If I remember well, I think I had the fixOwnership and it might have caused some issue when I tried AWS, so @pditommaso told me to use this docker.runOptions = '-u $(id -u):$(id -g)'.
And no problem with Docker on AWS, but haven't tried kubernetes yet ;-)

[pditommaso]

why is this not the default in Nextflow?

Well, this was a long discussion (with myself). To summarise the idea was to make it the default, but then I've realised that when using that setting also the container USER and home path are different that potentially could have some negative side effects

nextflow-io/nextflow#515

Still need to evaluate pros&cons.

[ewels]

this was a long discussion (with myself)

I know the feeling 😅

I'd be tempted to leave this out of nf-core pipelines for now then - same risk of pros & cons and could be resolved in a future core nextflow release anyway.

[ewels]

Closing for now @maxulysse - hope that's ok! Maybe submit a PR with some documentation describing this and how to fix with a user config under a troubleshooting section?

[maxulysse]

Ah, yes, I had questions, that's why I didn't merge it.
Sorry that I forgot to merge