Fix filename inconsistency

[tracelail]

Fixes #719 — removes double-underscore in output filenames for contrasts without a blocking variable and implements a canonical separator before the method name to . for output files.

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!
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir ).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir ).
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).