How to build a data analysis pipeline procedure
Nomially, I would simply just try to write a bash script (or powershell in windows) and just string the commands together.  However, this approach is rather fragile as in things get overwritten, and if it's an end to end process that has long batches.

I tend to use a workflow packages like luigi or airflow when stringing dependent task together.  The idea for Luigi is that you can break each action into a task.  Each task has three needed functions.


Requirement - what needs to exist before this task runs?
Output - where is the output going?
Run - what is the task?


So essentially you just chain a bunch of task and define your run function to call your previously built scripts using something like subprocess.  In requirement, you would reference the last step, and for output you would point towards where the file is being written.

The pro for doing this is that if your process breaks in task 50 out of 100, you don't have to rerun all 50 task, luigi will go down the dependency tree until it finds a requirement not fulfilled.  

Calling R from Pytho 
Luigi