The following terminal commands can be used to execute this demo script.
Step 1: Activate conda and snakemake
$ conda activate base
$ conda activate snakemake
Step 2: Download the snakemake-with-R folder and change directory accordingly
$ cd /path/to/snakemake-with-R
The folder snakemake-with-R contains the Snakefile, which contains the snakemake rules from which we can execute our R scripts. The folder scr contains two R scripts that show two different ways how variables can be passed between R and snakemake. The folder data contains a simple vector that is multiplied by the snakemake rules.
Step 3: Execute R scripts in the snakemake rules
First, you can perform a dry run of Snakemake with:
$ snakemake -n
For the two different ways how variables can be passed between R and snakemake, there are two different Snakemake rules. You can execute them as follows:
$ snakemake --cores 1 simple_test_rule
or
$ snakemake --cores 1 test_rule
The output is a simple multplication of the imput vector.
From here, you can make your workflow arbitrarily complex - enjoy.