Update docs for output paths, plugins, and consensus Document that Nextflow report paths ignore params-file overrides of output.directory, pin plugin versions for offline installs, correct the mapping.mapper parameter name, and clarify consensus/merge behavior. Signed-off-by: doc-maintainer <doc-maintainer@example.com>
Rewrite wiki documentation for the 4.0.0 release Add dedicated pages for the pipeline overview, inputs and reference, consensus model, operations and troubleshooting, testing, and the developer guide, and add a sidebar for navigation. Update the CLI, output, merge and installation pages to reflect the current parameters, validation behavior, reference representation, degraded caller mode and resource settings.