Pytest with nftest

[SPPearce]

In #7365 @GallVp was converting pytest to nftest for krona/ktimporttaxonomy, but it turns out it already had pytest files.

So I spent some time to check issues with the pytest files and found:

• Entries in pytest_modules.yml that had no corresponding modules or subworkflow file at all (e.g. gatk4/selectsamples)
• Entries in pytest_modules.yml that no longer had any pytest files (e.g. angsd/contamination)
• Modules with pytest and nf-test files, sometimes present in pytest_modules.yml but sometimes not.

In total this removes 18 entries from pytest_modules.yml, plus some more subfolders that weren't listed in there.

[GallVp]

Thank you @SPPearce

I was about to do something similar and then I saw the email notification for this PR.