Update all nf-tests to follow template v3.3.1 more closely

[d4straub]

Tests (*.nf.test) & test snaps (*.nf.test.snap) are updated to follow the nf-core template more closely and capture all produced files.

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/ampliseq 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).

[erikrikarddaniel]

👍

Interesting that you get so many stable files, even the binary .rds.

[d4straub]

Thanks!
Yes, most steps before taxonomic classification produce stable files.