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Question RE: best way to organize multiple entrypoints to a common WDL code base #433
Description
Hello, I had what is hopefully a quick question about the best way to handle large projects with multiple WDL entry points in AGC.
If we have a bunch of workflows that are importing from common WDL task files etc, is there a best practices for defining those different workflows to AGC?
My initial approach was to have a staging directory where each workflow entrypoint WDL would be symlinked in a directory corresponding to that workflow and in that directory have inputs.json and MANIFEST.yaml files. The problem there being that it seems like AGC doesn't then follow those symlinks when doing imports for the WDL. (i.e. if my workflow WDL MyExampleWorkflow imports a task WDL file with import "example_tasks.wdl", AGC will fail due to not being able to find example_tasks.wdl in the staging directory.)
Is there a preferred way of managing this that I'm not thinking of?
Thanks in advance!
Activity
markjschreiber commentedon Jun 13, 2022
Following SIM links might be a feature request although there are some implications as AGC will traverse nested directories.
One possible work around would be to have a github repo of common WDL subworkflows and for each workflow you
git clonethat into a sub-directory of the workflow.