update pipeline level test

[CaroAMN]

adding pipeline level tests, default.nf.test running the complete workflow (preprocessing + unet quantification on gpu)

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/lsmquant branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[CaroAMN]

• nf-test runs locally with singularity with the same command as on ci ( same profiles)
• pipeline runs with test and gpu profile with singularity locally
• nf-test for the numorph3dunet module passes on ci with singularity, gpu and small test dataset ( no stub run)

[d4straub]

Just a few comments. Looks like huge success on test!

[d4straub]

I got an email that says:

[...] The selected style seems to affect the size.
To fix that, please remove the 'style=plastic&' from the link to the badge's image (retaining the leading '?')
![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo)

Not sure if thats really an improvement though

[CaroAMN]

will change it in the next PR :)

[d4straub]

thats a module test, not a pipeline test, isnt it? Because the title of the PR is "pipeline level test" ...

[CaroAMN]

Yes its a module test. Yes, the intention of the PR was to update pipeline level tests ( adding + updating). Then i had some issues and on the way fixing them i started to fix other issues that i oversaw or forgot 🫣

[d4straub]

I find it admirable that you have meta.yml and .nf.test files for local modules and subworkflows, are you planning to add those to nf-core/modules or subsowrkflows? Because it seems like a fairly small step from here?

[CaroAMN]

Hm good question. My initial plan was not to. I just wanted to stick to the convention 😅

[CaroAMN]

Just a few comments. Looks like huge success on test!

Thank you so much for your review and taking the time to look at it! 🙏