This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Discovering absolute paths in runtime
I have a task that needs to remain unchanged that takes as an input a list of files to process. When I create the list myself, I put the absolute paths and everything is linked properly when running with Cromwell. When I try to put a task before it which actually creates the file list, the problem arises that at runtime the previous task defines the absolute paths based on its own Docker, and I need to know the "real" absolute paths of the filesystem, because the next task is not using the same container. The absolute paths created by the previous task no longer exist.
Because I am not allowed to change the following task, I cannot hack it with an archive with the said files, nor add preprocessing of paths in the line.
One idea is to use ../../old_task/execution/* structure, but that seems awfully dirty.
Can one somehow predict/find/construct at runtime the absolute paths of output files of any task, as seen on that filesystem?