Step Template to Run an R Script

Contrary to step_tmpl_do_call_script, this function copies the content of the script to the workflow folder. Therefore, the script do not have to exist on the HPC when using this template.

Usage

step_tmpl_rscript(r_script, setup_lines = NULL)

Arguments

r_script

The R script to be run by the workflow step

setup_lines

(optional) a vector of bash lines to be run first. This can be used to load the required modules (like R, python, etc).

Value

a template function to be used by add_workflow_step

Step Template

Step Templates are helper functions to be used within add_workflow_step. Some basic ones are provided by the slurmworkflow package. They instruct the workflow to run either a bash script, a set of bash lines given as a character vector or an R script. Additional Step Templates can be created to simplify specific tasks. The easiest way to do so is as wrappers around existing templates.