Hi there,

Thank you very much for all your efforts to make systemPipeR. I am new to this tool and have a possibly stupid question. Upon running the code for the quickstart guide (Section 2) found in

http://bioconductor.org/packages/release/bioc/vignettes/systemPipeR/inst/doc/systemPipeR.html#3_Getting_Started

the subdirectories data, param and results are created both in and outside the folder spr_project specified in the argument mydirmame of the functiongenWorkenvir(). The folders created oustide spr_project are mostly empty , whereas those inside have the dummy data.

Also the files batchtools.slurm.tmpl, targets.txt, and targetsPEC.txt are all created in both the folder spr_project and subdirectory spr_project/param

Why are these folders and files duplicated?

Thanks