@@ -13,6 +13,8 @@ Therefore, workflows have the following parts:
4. Set up of specific variables for the tools
5.`rule all` to specify what is/are the specific file(s) expected from the workflow.
> **Note**: These workflows are not made to be fully portable and reusable but at least give around 80% of the work done. You might need to do minor modifications. The idea being to have a copy of `Snakefile` workflow with its dedicated `config.yaml` file for each experiments.
### 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`.
This is a simple example of a workflow using metaphlan2.
## Example
An example is provided and is based on the `config.yaml` file. Singularity images are necessary for this example as well as the samples in the appropriate folder.