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Standardised parameters |
Strive to have standardised usage. |
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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