Check Inline Code Formatting

Review inline code in markdown files for proper formatting and appropriate use of syntax highlighting.

See ../shared/repo-conventions.md for file conventions.

What to Check

1. Missing Backticks

The following should always be wrapped in backticks:

CLI flags and options:

• -resume, -profile, -params-file, --input, etc.

Filenames and paths:

• nextflow.config, .command.sh, work/, modules/, etc.