Command Line Options¶
This section explores the different options that are possible when running the tool. Before running the tool, you can first run the command mitopipeline -d in order to download all of the dependencies necessary for the steps in your pipeline if you do not specify a tools directory.
Downloading Software¶
| Option | Description |
|---|---|
-d or --download |
REQUIRED.
Option to download softwares for steps not listed in -r.
|
-r or --remove |
Specifies steps that won’t be run in the pipeline.
Input: <name of steps>
Default: None
|