Running commands with Snakemake


Running Python code with Snakemake


Placeholders and wildcards


Chaining rules


Figure 1

A visual representation of the above process showing the rule definitions, with arrows added to indicate the order wildcards and placeholders are substituted. Blue arrows start from the input of the `plot_avg_plaquette` rule, which are the files `intermediary_data/beta1.8/pg.plaquette.json.gz`, `intermediary_data/beta2.0/pg.plaquette.json.gz`, and `intermediary_data/beta2.2/pg.plaquette.json.gz`, then point down from components of the filename to wildcards in the output of the `avg_plaquette` rule. Orange arrows then track back up through the shell parts of both rules, where the placeholders are, and finally back to the target output filename at the top.

Metadata and parameters


Figure 1

Screenshot of a spreadsheet application showing the file metadata/ensemble_metadata.csv.
Screenshot of a spreadsheet application showing the file metadata/ensemble_metadata.csv.

Multiple inputs and outputs


How Snakemake plans jobs


Figure 1

TODO
TODO

Optimising workflow performance


Figure 1