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.
For more information, check here.
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. The
Snakefileis located inside the input folder and must have a unique name (this is relevant in case there are multiple
Snakefilefiles linked together).
For information on how to use the Additional dependencies 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 about how to manage Conda environments in Snakemake, check the official documentation.
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.