I want the input ref used in analysis toolkit, and the toolkit input the ref in config format,not in command-line format.Then,How can I deal with it,when I use CWL .
Your question is too vague and badly written. For people here to help you, you need to explain what you are asking in a well structured way
Please read these post and re-frame the question
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And I want to know. when cwl running in a docker ,where is the running dir and the input files dir copied to the same dir?
My software need the ref directory name，and I need assign the directory name by cwl-yaml's ref params.How can I achieve it？
It is really difficult to understand what the issue is. Maybe try giving us a specific example of what you are working on. What software do you want to run? Can you post the current version of your command line tool, even if it doesn't work? What is the file you have trouble passing to the tool?
If you put a little more effort into elaborating, i am sure we will be able to help.
Sorry for my obscure expression. I have made it.
For creating configuration files at runtime, please consult this part of the CWL User Guide: https://www.commonwl.org/user_guide/14-runtime/index.html
Yes,I have made it. Another quesiton: How can I write inputs to support the one options or more repeats arguments. For example :"-L chr1" and "-L chr1 -L chr2 -L chr3".
hoping your reply,not vote... Thanks!