Getting started with Snakemake
In this part of Exercise 1, we’ve seen:
- how to get file names from the file system directly (o1)
- how to use a configuration file to specify paths and parameters outside of the code (o2)
- more about specifying directive values & ways of calling them within the shell directive (o2)
- quick demo on how to integrate your Python skills into Snakemake (o2)
- how to redirect stdout and stderr streams (log) (o3)
- re-running options (o4)
Some more useful options when running Snakemake
– print the reason for each rule execution:
-r --reason (for Snakemake version <8 only)– print a summary and status of a rule:
-D– automatically create HTML reports (
--report report.html) containing runtime statistics, a visualisation of the workflow topology, used software and data provenance information (need to add the jinja2 package as a dependency)
all Snakemake optionsIn the last part (part C) of this Exercise, we will see how to adapt your pipeline to an HPC environment:
- how to upscale your pipeline
- how to control the resources used
- how to control the software environment used