Release PR: dev to master

[chaochaowong]

pacvar 1.1.0, Kākāpō Awakens, expands the WGS workflow with new copy number variant (hificnv), structural variant (sawfish), 5mC methylation (pb-CpG-tools), Fiber-seq 6mA preprocessing (fibertools), and variant annotation (Ensembl VEP) capabilities. This release also updates the pipeline template to nf-core/tools 4.0.2 and refreshes core nf-core modules and infrastructure.

Notes:

• skip_fiberseq=true by default because most PacBio long-read WGS datasets are generally not using the Fiber-seq protocol for N6-methyladenosine (m6A) detection. Fiber-seq is mainly relevant for epigenetic or chromatin-focused studies.
• I am not updating the most current hiphase (v1.6.0) module in this PR because doing so would require changes to the pipeline flow and would involve substantial additional work.

Future work for v1.2.0:

• Update the hiphase module to v1.6.0 to support both SNV and SV inputs for haplotype phasing.
• Add support for Ensembl VEP --plugin and --custom options.

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/pacvar 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).