Hello, I am looking to define a default value for a file input (metadata in the below example) in a CWL tool definition, using value of another input. I’ve seen examples for constructing string inputs using javascript but not sure if I can do something similar for File inputs. Wanted to check if s…

If this input directory contains only a few files/folders and they have separate value to the workflow (either because you reuse them without the rest of the directory later, or you want to assemble this input directory from components) then you might want to consider making them explicit separate i…

Hello Sehrish, Seems like this tool description is passing an entire directory to the tool and that you want to specify a single file within it for a particular command line option. This is a bit irregular for CWL. Ideally each individual file or groups of files would have their own inputs. Can yo…

Hi Michael, Thanks for the response. The tool definition I am working on expects a directory input. metadata is one of the files inside this directory for which there can be a default value that can be extracted from the path that is specified for inputDir. Example If my input value for inputDir …

Thanks a lot, Michael. For this particular tool, the second option (using arguments) would work best. The input directory has quite a few number of files (raw sequencing data - bcls). One of those files is something.csv for which there is always a fixed location. So I thought to rather set a defau…

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Constructing a default value for a tool input

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