Using configuration files (json/yaml) to control multiple steps of a CWL workflow

CWL Questions
1

Hello!
I’m fairly new to using CWL and am wondering how to do the following (this is a hypothetical situation): I have data files that I’d like to run a workflow on, and this workflow has several user chosen parameters for the tools. Instead of hardcoding those in, I’d like to have a configuration file that contains the values of those parameters. This way, if I want to change some of my workflow settings, all I need to do is change the configuration.

Happy to provide more details if needed!
Thanks!

2

Hi!

You can use a YAML file as an input file which can serve as your configuration file I guess.
https://www.commonwl.org/user_guide/topics/inputs.html

(see the " inp-job.yml" example)

Here you can set any input that you have defined in the inputs section of your workflow.
This however also means that you will have to define your input files as well in this yaml file.

Hope this helped.
Bart.

1 Like
3

I see, thank you! This is what I was looking for!