Getting started with Snakemake
For this practical exercise, we will:
- learn how to get file names from the file system directly using glob_wildcards (o1)
- learn how to use a configuration file to specify paths and parameters outside of the code (o2)
- learn more about specifying directive values & ways of calling them within the shell directive (o2)
- bonus: we will see a quick demo on how to integrate your Python skills into Snakemake (o2)
- learn how to redirect stdout and stderr streams (log) (o3)
- learn more about re-running options (o4)
In the following objectives, we will be building on the Snakefile from Exercise 1A which successively runs FastQC then MultiQC on a set of RNA-seq data.
How this exercise is organised:
Each step will reply to an objective. Thus, we will be doing several cycles of executing snakemake, observing the results and improving the code. Each code version will be noted ex1b_oX.smk, with X a progressive digit corresponding to the objective number.