I do a lot of scripting in R, and with ggplot2 and bioconductor; there is so much one can achieve. Pipelining was surely a issue, so we built a tool to do just that (http://docs.flowr.space). One starts with a bunch of system commands, wraps them into a tab-delim text file. When done flowr can submit to a local server (parallel using mclapply), and clusters like LSF, Torque, SLURM and MOAB etc...
flowr function [arguments]
status Detailed status of a flow(s).
rerun rerun a previously failed flow kill
Kill the flow, upon providing working directory
fetch_pipes Checking what modules and pipelines are available;
Please use 'flowr -h function' to obtain further information about the usage of a specific function.
Certainly biased (being a developer) but one may find it much easier to create a tsv file, than learning new syntax.
Second issue I faced was, say I have a R function which does a lot of things and now I wanted to call it from the terminal. R does not have a nice standard argument parse like python/perl. Now we have a package funr, where the first argument is the function you want to call, and rest are its arguments. One can call any R function of any installed package (or sourced script).
funr rnorm n=10
-1.244571 1.378112 0.02189023 -0.3723951 0.282709 -0.22854 -0.8476185 0.3222024 0.08937781 -0.4985827
Hope you find it useful. Would be curious if it works out.
I appreciate that you are trying to get some general advice before setting out on a task, but this is a very general question. You will probably get more help if you can provide some specifics about what you plan to do (what task are you automating, how do you plan to achieve each step).