Supernova sample parmameter

Posted By: graham, on Jun 21, 2019 at 4:23 AM


I have 10x data from one sample over three different libraries, all located in the same directory. When I run Supernova 2.0.1 I get the following error:

The --sample argument must be specified if multiple samples were demultiplexed in a run folder. Options:


But, the help page states that by default, all samples are used:

--sample(optional) Can be used to select only a single sample of those specified in the sample sheet supplied to mkfastq. By default, all samples are used.


I managed to get around this by specifying:


in my Supernova script, but I wonder why it's described as optional in the docs, but turns out to be mandatory in the code.

Dr. Graham Etherington
The Earlham Institute, Norwich, UK
Twitter: @bioinformatiks