Snakemake

Snakemake type access

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Snakemake type access

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Snakemake type access

Snakemake type access

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.

Input parameters

The app has one mandatory parameter which allows to import the directory the snakemake command is executed in. By default, Snakemake will search for Snakefile, snakefile, workflow/Snakefile, workflow/snakefile beneath this directory, in this order.

The user can specify another path for Snakefile using the corresponding optional parameter.

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.

Multiple environments

The user can also install the required software dependencies in separate environments via conda or mamba by specifying the path(s) to the corresponding configuration YAML file(s) directly in the Snakefile. In this case the user must use the option --sdm conda.

For more information about how to manage 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.