Unify summarised experiment

[atrigila]

Closes #1465

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/rnaseq 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).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[atrigila]

The template has to be merged first.
I also need to update the tests here.

[atrigila]

Tests are not being triggered automatically so I'll test the solution of closing and opening the ticket.

[atrigila]

24.04.2 tests are OK but latest-everything tests are failing because we require the template to be merged first.

[pinin4fjords]

Sorry, been a busy couple of days, will try to resolve the template tomorrow.

[atrigila]

No worries, no rush at all. I could also give a hand with the template if I have some time these days as well :)

[pinin4fjords]

So this is good now then?

Only thing I might suggest is some R code example somewhere in the docs illustrating how to access the different assay slots of that object.