Template: replace docker.runOptions by containerOptions

[mirpedrol]

Since userEmulation was deprecated from Nextflow, we recently added docker.runOptions = '-u $(id -u):$(id -g)' to the pipeline template for profiles docker and arm.
The problem of this is that it can't be overridden in one single process.

Instead, we can use 'containerOptions' which will allow us to override the option with modules.config.
See an example in crisprseq, where we were finding some permission errors in the containers and this solved the issue.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (31c61ca) 73.41% compared to head (0a895b5) 73.27%.

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