Nf core template merge 3.3.1

[d4straub]

Merging template update 2.3.1.

Tests are working. I simply made the previous/primal implementation of nf-test in ampliseq work with the current template 3.3.1 setting. That means that the snapshots are not generated with nf-test but manually with selected 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).

[d4straub]

The following errors occur in tests:

'-profile test_failed' 
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (treatment1--2)'
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (treatment1--3)'

'-profile test_sintax'
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1)'
    > Command exit status:
    >   125
docker: failed to register layer: write /usr/local/libexec/gcc/x86_64-conda-linux-gnu/13.1.0/cc1plus: no space left on device

'-profile test_failed' also failed in the previous attempt in #859, but '-profile test_sintax' succeeded there.

[d4straub]

By increasing the number of shards '-profile test_sintax' passes now.

[d4straub]

'-profile test_failed' still fails with the mysterious
Process `NFCORE_AMPLISEQ:AMPLISEQ:QIIME2_ANCOM:QIIME2_ANCOMBC_TAX (treatment1--3)` terminated with an error exit status (1)

[jfy133]

A couple of comments but overall LGTM, fine workaround for the syntax differenece in the .nf.test files

[jfy133]

Is this on purpose?

[d4straub]

Yes, because for an unknown reason that makes the test fail. That param is also activated (and succeeding) in profile test, so I am not overly concerned about it fr now.

[d4straub]

Thanks for the review!