Remove custom docker.runOptions from nextflow.configs living in tests folders

Some modules supply their own docker.runOptions. This is a relict.

https://github.com/search?q=repo%3Anf-core%2Fmodules%20docker.runOptions&type=code

For gatk4spark modules however this might still be needed:

@mahesh-panchal:

I think I have a lead, but I’m not sure what to do about it at the moment. I think the reason spark is not working with the user id and group id passed through docker is because spark wants an entry for it in /etc/passwd. The normal entry point for the docker container I believe has a mechanism to add one:
https://github.com/apache/spark/blob/cef665004847c4cc2c5b0be9ef29ea5510c0922e/reso[…]gers/kubernetes/docker/src/main/dockerfiles/spark/entrypoint.sh
Nextflow however overrides the entrypoint in the .command.run so it calls bash instead.
The docker.userEmulation = true also imports /etc/passwd so perhaps something could be done with beforescript

For other modules we want to remove those.

Start with the repository code search for docker.runOptions in nextflow.configs under tests folders. Review the single comment and compare gatk4spark modules separately, since that exception is unresolved. Done means removing the obsolete options from other modules while retaining any confirmed Spark requirement and keeping the affected tests valid.