Release 2.2.2

[charles-plessy]

This is a technical release upgrading the template to version 3.5.1 and removing versions.yml files. Here is the full changelog:

v2.2.2 "Juicy" - [January 26th 2026]

Fixed

• Conforms to nf-core template version 3.5.1 (https://nf-co.re/blog/2025/tools-3_5_0)[#95](https://github.com/nf-core/pairgenomealign/issues/95)[#98](https://github.com/nf-core/pairgenomealign/issues/98).
• Fixed nf-core logo (#90).
• Adjusted process requirements to test_full case (#61).
• Set an icon in the --targetName option in the documentation (#92).
• Fixed a bug of last/train records the wrong value for percent identity (#96).
• Merged output channels in last/dotplot (#100)
• Created missing meta.yml for subworkflows (#101).

Dependencies

Dependency	Old version	New version
assemblyscan	0.4.1	1.0.0
MultiQC	1.30	1.33

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/pairgenomealign 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).

[jfy133]

Approval after reviewing the previous PR: #99, can be merged once tests pass!

[charles-plessy]

@jfy133 We made the tests pass by excluding the PNG files from the pipeline tests in 22f70db but if that was too heavy-handed, please let us know and we will fix that in the next release.