replace local/medaca with nf-core/medaka and add busco output to multiqc

[Daniel-VM]

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/bacass branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
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• 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).

PR description

• Replaced the local Medaka module with nf-core/medaka.
• Updated modules.json and bacass.nf to use the nf-core module.
• Removed manual ch_versions handling, since versions are now collected via topic-based channels.
• Added BUSCO to MultiQC reports for short, long, and hybrid assemblies.
• Updated MultiQC module order and report section order to include BUSCO after QUAST.

(The BUSCO outputs were already being staged into the muliqc output, but the per-assembly-type Multiqc configs were filtering them out. This is now fixed.)

[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: 3.5.2.
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.