Automatic execution of consecutive analysis steps. Especially useful for analyzing many spectral files across multiple experimental conditions, see this [tutorial](https://github.com/Nesvilab/philosopher/wiki/Pipeline-mode-for-TMT-analysis) for more information.


## Usage

`philosopher pipeline [flags] [folders]`


## Flags

`--config`

Configuration file for the pipeline execution.

`--print`

Print the pipeline configuration file.


## Example


`philosopher pipeline --config philosopher.yaml folder1/ folder2/ folder3`


## FAQ

_How do I set the steps I want to run ?_

Your configuration file (philosopher.yaml) contains the steps you want to execute and
their respective parameters. You need to change the steps from _no_ to _yes_ in order to include them
in your analysis. After that, check the parameters within each section and customize them for your analysis.