Reference¶

Reference pages provide complete, terse technical descriptions. Use them to look things up: every config key, every output file, every CLI flag.

• Config schema: Every config.yaml key, its type, default, and description.
• Sample sheet schema: Column specifications for the samples CSV.
• Output files: All output files with path pattern, format, and when produced.
• CLI flags: Snakemake invocation flags relevant to snpArcher.
• Modules: Module registry covering QC and postprocess.
• Changelog: Release history and migration notes.