Removing docker.userEmulation from config

[Lfulcrum]

It looks like docker.userEmulation is no longer supported from nextflow 24.01.0.

There was some discussion on what to do about this here:
https://nextflow.slack.com/archives/C02T98A23U7/p1709049357728229

It looks like our options are to either remove it or to add settings similar to what docker.userEmulation achieved via docker.runOptions or process.containerOptions (less desirable).

According to https://nextflow.slack.com/archives/C02T98A23U7/p1696591307155289?thread_ts=1696590982.727319&cid=C02T98A23U7, it apparently used to add the following arguments to the docker invocation:

-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME

I'm suggesting that we just remove it in the hope that it was never truly required by any of our pipelines. That said, according to the discussions above, it could be that GATK requires:

docker.runOptions = '-u $(id -u):$(id -g)'

So we might need to test with a pipeline that users GATK if we want to be more confident that it's not required for that.

[Lfulcrum]

Not so urgent I think - the user will only get a warning like:

WARN: Undocumented setting `docker.userEmulation` is not supported any more - please remove it from your config

when running a pipeline via nextflow >24.01.0

[flass]

hmm I think we need to think this a bit more carefully so I suggest we park this until next week when we are all in to assess