Minor fixes, update miniprot params and synteny path

[weaglesBio]

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/treeval branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile 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).