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Supernova sample parmameter

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

Hi,

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:
PRO2044_S1_Steppe_LIB36621
PRO2044_S1_Steppe_LIB36622
PRO2044_S1_Steppe_LIB36623

 

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:

--sample=PRO2044_S1_Steppe_LIB36621,PRO2044_S1_Steppe_LIB36622,PRO2044_S1_Steppe_LIB36623 

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