Webgestalt: Organism is missing Error

[hoelzer]

When running the pipeline the Webgestalt process fails because of

Organism is missing.
Error in idMappingGene(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile,  :
  Organism is missing.

I am using Homo sapiens. I also tried the webgestalt.R script manually and althought hsapiens is defined as organism in this line

https://github.com/hoelzer-lab/rnaflow/blob/master/bin/webgestalt.R#L18

it fails.

Could it be that this is because the variable organism is never before initiated outside of the IF-ELSE? Ah no, this can not be the reason because if the variable would be NA the whole process would never start. So it is set to hsapiens

[fischer-hub]

Will check!

[hoelzer]

I think we might not have noticed this bc/ of the error catch in the script that also catches this problem.