Snakemake¶
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Extension:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Extension:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Utility:
Extension:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Operating System:
Terminal:
Shell:
Editor:
Package Manager:
Programming Language:
Database:
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
Select input parameters¶
The app has two mandatory parameters:
Input folder: it mounts the folder containing source code and input files.
Snakefile: it selects the principal
Snakefilefile with the workflow instructions. TheSnakefileis located inside the input folder and must have a unique name (this is relevant in case there are multipleSnakefilefiles linked together).
Initialization¶
For information on how to use the Initialization parameter, please refer to the Initialization - Bash script, Initialization - Conda packages, and Initialization - pip packages section of the documentation.
Create a Conda environment¶
The user can also install the required software dependencies via Conda by specifying the path(s) to the configuration YAML file(s) directly in the Snakefile. In this case the user must use the option --use-conda. For more information about how to manage Conda environments in Snakemake, check the official Snakemake documentation.
Interactive mode¶
The Interactive mode parameter is used to start an interactive job session where the user can open a terminal window from the job progress page and execute shell commands.
Snakemake GUI¶
By selecting the option -g, an HTML-based user interface is accessible through the button
Note
It is strongly recommended to avoid usage of the --use-conda option of Snakemake and GUI simultaneously. Instead, the Initialization parameter should be used to install software dependencies with Conda.
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