syqada begin

SyQADA will try to help with initial preparations for a project if you invoke:

>>> syqada begin

This will show you a list of the protocols currently available. If you select one of these by number, SyQADA will then create a control directory, ask you for a project name, and create the three project files you need to run the workflow. You may not need to edit the protocol file, but you will almost certainly need to edit the config file, you’ll need to create your own samples file.

For most protocols, the config file will include all the parameters including a sourcedata specification that you need to specify for a successful run.

The sample can be a simple list of your samples, or it may have a header line that specifies optional phenotypic attributes. Further description of these three files is found on the syqada auto manual page.