Dev

[charles-plessy]

I plan to use the same release name as I like Tokoroten and 3 days is too short for changing it.

v3.0.1 "Tokoroten" - [June 29th 2026]

Fixed

• Fix strict syntax error when using --multi-cram.
• Run the long test with the RY4 seed and --multi-cram as a better showcase.

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).

[nourmahfel]

Looks good to me :)