Tools

This directory contains all tool descriptions that can be imported and used within Snakemake workflows.

Design and best practices

All tools are described in a Snakefile in a directory having its name. All Snakefiles try to respect some rules and best practices in their design:

• Reference to options from a config_example.yaml file
• Tool description

Reference to options from config.yaml file

First part correspond to all options that are set up from a config.yaml file. They all have the nomenclature __TOOLNAME_variable.

Then in the YAML config_example.yaml file, you can set the variable as followed:

TOOLNAME:
  variable: 4

We recommend to use the get method to access this parameter and set a default value:

config['TOOLNAME'].get('variable', 1)

Tool description

In order to ease the linking of tools in a workflow, every parts of the tool is described as followed:

• input with the nomenclature: __TOOLNAME_input
• output with the nomenclature: __TOOLNAME_output
• params with different options that are described above
  • There is usually a exec_command to give the possibility to change the way the tool is called (locally installed, singularity ...)
  • There is usually a options to specify all other command line options. You can still give a more detailed level of description for the options
• the shell command

input and output are then set up in the workflow Snakefile that refer to the rule. Therefore the rules cannot be used directly.

Info: You have noticed the possibility to give modules this is dedicated to our HPC that have some tools accessible via module.

Example

To find out example, refer to the workflow based on this tool descriptions in the /workflows/ section.