Standardised parameters

The key words “MUST”, “MUST NOT”, “SHOULD”, etc. are to be interpreted as described in RFC 2119.

Pipelines SHOULD use the same command line option names as other pipelines for comparable options where possible. For example, --input and --genome.

Parameter names SHOULD work in a similar way across pipelines. For example, --input typically takes a .csv sample sheet file where appropriate.

We’re planning to build a tool that lists every parameter used by every pipeline, so that you can check for existing parameters with similar names You can track the progress of this feature request here: nf-core/website#1251