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SnakeTools

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

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.