Provide a simple interface to query the input and output files of a snake workflow. This allows snakemake to be used as part of the workflow or execute indepedently as scripts. This enables the development of snakemake scripts in jupyter notebook or vscode code cells, significantly improving the development efficiency.
The original snakemake will inject a snakemake object into the running script, which will be confused with the snakemake package if you are running the sccript outside of the snakemake environment. This helper function compile the workflow and extract the input and output file names for you, so that you can use them to develop the script outside of the snakemake environment (e.g. in a Jupyter notebook or interactive shell). It uses the variables returned by local() function to determine whether it is running in a snakemake environment, and if so, return the input and output from the snakemake object. This provide a seamless development workflow where the same script can be run both inside and outside of snakemake, making code iteratiion and debugging much easier.
Due to the requirement of snakemake on the datrie package, in Windows you will need to install the Microsoft Build Tool for the setup to be successfully. Download the run the installer. Click modify
Ensure that the C++ tools are installed
Next clone the repository and then install via pip
git clone https://github.com/teristam/snakehelper.git
cd snakehelper
pip install .
def getSnake(locals:dict,snakefile:str, targets:list, rule:str, createFolder:bool = True):
"""Return the input and output files according to a snakemake file, target and running rule
Args:
locals (dict): Local variables dictionary of caller script
snakefile (str): Snakefile location
targets (list): The file or files that are created when the rule is executed
rule (str): The rule for which you want to determine the input and output files
createFolder (bool): Whether or not to create output folders. Default is True.
Returns:
Tuple: A tuple of dictionaries containing input and output file names, as defined in the snakemake file.
"""
from snakehelper.SnakeIOHelper import getSnake
(sinput, soutput) = getSnake(locals(), 'tests/make_files/workflow_common.smk',
['tests/processed/recording_info.pkl'],'sort_spikes')
snakemake require you to specify at least one of the output file name so that it can extract the wildcards used to build the workflow.
sinput and soutput are dictionaries containing the input and output file name from the sort_spikes rule. getSnake will automatically determinate if it is inside the snakemake environment or it is run as an standalone script.
When you run getSnake in the Python interactive cell in VS Code, by default it will open the shell at the folder of the Python script. However, in many cases, the Snakemake files are defined relative to the project root folder. You can either change the working directory of the interactive shell to the project root folder, or you can define the project root directory in the SNAKEMAKE_DEBUG_ROOT environment variable and getSnake will automatically switch the working directory to that folder. Alternatively, you can also define the environment variable in a .env file in the project root directory and VS Code will automatically load it when it opens the interactive window. Note that the .env file will not be automatically loaded if you run the Python script outside of VS Code. In that case, you need to define the environmental variable manually according to the methods commonly used for your operating system.