Standardised parameters

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

In addition to the names of parameters, they should ideally work in a similar way. For example, --input typically takes a .csv sample sheet file (but not always, where not 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