Document how to display the full list of SPEAQeasy options

LieberInstitute · Sep 20, 2023 · 7923c57 · 7923c57
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diff --git a/documentation/03-All_Command_Options.Rmd b/documentation/03-All_Command_Options.Rmd
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 ## SPEAQeasy Options
 
+On the command line inside the `SPEAQeasy` repository, one can run `Software/nextflow run main.nf --help` (at JHPCE, `nextflow run main.nf --help`) to display the full list of SPEAQeasy options.
+
 ### Mandatory Parameters
 
 * `--sample`        "single" or "paired": the orientation of your reads