Add kivvi module

[sofiademmou]

PR checklist

This PR adds a new nf-core module for kivvi.
Closes #13089

• 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 module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[erikrikarddaniel]

Reviewed with Claude Code.

Thanks for adding kivvi!
I ran v1.1.0 from the module's container on the two example bamlets (twice for kiv2, to check which outputs are stable).

The main thing: the module only emits the realigned BAM, but kivvi's results are the JSON report (copy number, alleles, variants) and the VCF; it also writes an SVG and a BAM index.
Suggestions inline for main.nf and the stub; meta.yml needs the same outputs.

Tests:

• The real tests read their bamlets from the main branch of the tool's own repository; they should come from nf-core/test-datasets.
• The JSON's supporting_reads lists change order between runs, so the JSON (and the SVG) need unstableKeys, and the copy number call itself is worth asserting (values inline).
• The "set outdir" stub test passes --out ./, which the module already sets, so it can't fail on its own.

Minor: the PR checklist is still all unticked.

[erikrikarddaniel]

Test data should come from nf-core/test-datasets (params.modules_testdata_base_path), like the stub tests below. These bamlets are on the main branch of the tool's own repository, which can change or move under the test.
Both are small (40 and 7 MB), so they could be added to test-datasets as they are.