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

Project description

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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.

v0.0.5 / 2017-10-10

  • requirements_dev.txt: update and pin reqs

  • flake8 fixes

  • tox.ini: simplified config

  • added flake8 to reqs

v0.0.4 / 2017-10-10

  • added preliminary test suite

  • Makefile: changed install to use pip install -e .

  • added example files for testing

  • requirements.txt: created with pipreqs

  • snaketools.py: reorder functions

  • snaketools.py: formatting

  • ignore .vscode/

  • pin all reqs since pyup now manages

v0.0.3 / 2017-09-15

  • Configure pyup

  • SnakeRun.d -> SnakeRune.interim_dir

v0.0.2 / 2017-09-06

  • fixed bumpversion artifact

  • errors.py: pulls metadata from top module

  • updated dev reqs for doc building

  • activated travis ci

  • Set up flake8 configuration

  • Docs build corrected

v0.0.1 / 2017-09-06

  • README.rst: added prelim description of features.

  • snaketools.py: fixed typo

  • Initial commit

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