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.
Change Log
v0.0.8 / 2018-06-08
stopped using pinned versions.
v0.0.7 / 2017-12-18
change pyup check to monthly
update reqs from PYUP
snaketools: SnakeRule now registers with SnakeRun
snaketools: added attr SnakeRule.extra for more params
snaketools: added attr SnakeRun.rules
snaketools: use __all__ for importing from file
update makefile
update reqs
v0.0.6 / 2017-10-26
added rewrite_snakefile_no_rules()
flake8
requirements.txt: removed dev-reqs
requirements.txt: pinned flake8
setup.py: upgraded to read from req files
MANIFEST.in: include req files
upgraded Makefile
tox.ini: set line-length etc
setup.cfg: ignore W292
setup.cfg: exclude lib & bin from flake8
updated .gitignore
added coveralls badge
HISTORY.rst: replaced header text
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
1 maintainer
Release files for snaketools 0.0.8
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