Nextflow strict syntax

[d4straub]

Prepare for Nextflow strict syntax:

• fixed all syntax errors
• fixed all syntax warnings in non-nf-core files (some warnings remain in nf-core suworkflows & modules)
• updated several nf-core modules & workflows to avoid errors and minimize warnings

Fixed that was before broken:

NXF_VER=25.10.3 nextflow lint . -exclude ".git,.nf-test,nf-test.config"
NXF_VER=25.12.0-edge NXF_SYNTAX_PARSER=v2 nextflow run . --help

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).
• 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).

[d4straub]

Short intermediate evaluation of CI tests

• 1, 2, 3: assembly files and multiqc files differ in md5 sums
• 4: multiqc file and fastp json md5sum changed
• 7: additional QUAST files, assembly & multiqc file md5 sums changed
• 8: kraken2 tool version mismatch
• 5,6,9: passing

[d4straub]

@nf-core-bot fix linting

[JoseEspinosa]

Just a small suggestion but otherwise LGTM 🚀

[JoseEspinosa]

LGTM! Thanks 🚀

[d4straub]

Thanks for the review!