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# Tools

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

Every rules for a tool should come with an example of use in a workflow as well as a `config.yaml`
example file (usually containing default parameters that are set up on the `.rules` file itself).
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## Design and best practices

All Snakemake tool descriptions try to respect some rules and best practices in their design:

* First part correspond to all options that are set up from a `config.yaml` file
* Then the tool itself is described with:
  * input with the nomenclature: `__TOOLNAME_input`
  * output with the nomenclature: ` __TOOLNAME_output`
  * params with different options that are described above

input and output are then set up in the Snakemake file that refer to the rule.