Include the reports in the package
This is more of a suggestion rather than something needed.
Move the actual reports from the NXFpipe2go repository into this package.
The reports would live in the inst
folder. Then, they could be accessed using bash directly from the filesystem, or ideally extracted from the package and rendered after the pipeline finishes with this simple R code:
file.copy(system.file("DEreport.Rmd", package="NXFpipe2goShinyReps"), "./reports")
rmarkdown::render("./reports/DEreport.Rmd")
Edited by Sayols Puig, Sergi