Fix foreground list

[hverdonk]

Fixes #1

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, add a test dataset to the test_data directory.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [N/A] Usage Documentation in docs/usage.md is updated.
• [N/A] Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

What changed

• Added a dedicated module to sanitize user-provided foreground taxa lists
  • Introduced the cleanforegroundlist module (CLEAN_FOREGROUND_LIST) to convert “messy” IDs in the foreground taxa list into HyPhy-compatible IDs by replacing non-alphanumeric characters with underscores.
  • Updated/added module tests and refreshed snapshots to reflect the module’s actual runtime environment / versions.
• Integrated foreground list sanitization into the viral non-recombinant subworkflow
  • Updated subworkflows/local/process_viral_nonrecombinant/main.nf to run CLEAN_FOREGROUND_LIST when --foreground_list is provided and pass the sanitized list into downstream labeling steps.
  • Updated the associated nf-tests to cover lists with “messy” unsanitized taxa IDs
• Hardened parameter validation for foreground_regexp
  • Added validation in subworkflows/local/utils_nfcore_capheine_pipeline/main.nf
    • --foreground_regexp can no longer be an empty string (e.g. "" / whitespace).
    • tightened handling around invalid types / invalid foreground list paths
• Docs + test data updates
  • Updated README parameter docs to clarify that matching/sanitization uses underscore escaping.
  • Added new test data for messy foreground sequences (pretend-foreground-seqs-messy.txt).
  • Cleaned up and re-enabled/adjusted relevant workflow/subworkflow tests after introducing the sanitization step.

Why

• Ensures foreground sequence selection works reliably with HyPhy’s sanitized taxon naming conventions.
• Prevents confusing “provided but empty” configurations for --foreground_regexp, which previously could slip through and cause failures after the pipeline had run several modules.
• Improves test coverage for realistic “messy ID” inputs and keeps module metadata up-to-date.

Testing / Validation

• nf-test module tests for cleanforegroundlist updated and passing (snapshots generated).
• Subworkflow nf-tests updated to include more foreground list + messy foreground list + regexp scenarios.