SnakeTools

Small library of helper tools for setting up, graphing, and working with Snakemake rules.

• Free software: MIT license
• Documentation: https://snaketools.readthedocs.io.

Features

• SnakeRun object to initialize and manage information common to the whole run, such as:

  • a copy of the config values from the config file provided to snakemake.
  • a place to store global variables needed throughout the run.
  • more

• SnakeRule object to manage the initialization and deployment of rule-specific information including:

  • the rule name
  • a default out directory deduced from the SnakeRun object
  • a default log file path
  • a “pretty name” for the rule to be displayed in the DAG graphs.
  • attributes that store the input, output, and params values for later use.
  • a copy of the values specific to this rule from the original configuration file.
  • more

• recode_graph function that cleans up the default output of snakemake --dag and allows the use of pretty names stored in the SnakeRule objects.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.