WDL workflow fails in Firecloud due to locating a directory but works in local cromwell environment

I have a WDL workflow that is based on Rscript and it works fine in local cromwell environment when I provide relative paths for the functions. But the same WDL fails in FireCloud. I was able to replicate the same error in local environment if I give the wrong directory to the R function. This makes me believe that FireCloud has problem finding the directory or using the wrong directory. How can I resolve this? Is there a way to provide absolute path to the directory and is it acceptable to provide absolute paths in FireCloud?