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