Scaffold DDA and Scaffold DIA have a full-featured command line interfaces (CLI) for interacting with the programs. In this guide, we will discuss the workflow file and how to use it to configure CLI batch processes.
See this PDF for more information on Scaffold DIA CLI Workflows:
https://cdn.proteomesoftware.net/documentation/scaffold_dia_workflows.pdf
See this PDF for more information on Scaffold DDA CLI Workflows::
https://cdn.proteomesoftware.net/documentation/scaffold_dda_workflows.pdf