Release 2.2.1 containing bug fixes and template update

[charles-plessy]

v2.2.1 "C’est quoi ça?" - [August 5th 2025]

"C’est quoi ça?" sounds like shiikwāsā, an iconic fruit in Okinawa.

This is a bugfix release and template update.

Fixed

• Conforms to nf-core template version 3.3.2, hopefully fixing AWS tests (#85) (#83).
• Added missing pipeline and subworkflow test snapshots and stabilise line order in some output files (#84).
• Update modules to latest version, thereby pulling an important fix for a race condition in last/mafconvert (#87), (#88).
• Report jq version used in MULTIQC_ASSEMBLYSCAN_PLOT_DATA (#81).
• Document module names in tube map (#74).
• Add mising modules in tube map (#68).
• Materialise output files in tube map (#75).

Dependencies

Dependency	Old version	New version
MultiQC	1.28	1.30

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).

[vagkaratzas]

LGTM! Guess we'll both just have to wait for a non-buggy conda MultiQC version now.

[maxulysse]

Pipeline logo on the subway map looks a bit off, a part all looks good to me