I've got a task that runs in docker and creates a fofn file. This fofn is then to be used as input for another task (not in docker). However, the filepaths in the fofn are relative to the cromwell-root and as such not accessible to the new task.
How could I fix this?
NB, this is an overly simplified situation sketch, but I think it gets across the message.
To be more specific, I'm trying to use the WDL `size()` directive to decide what to do with each file in the fofn.
Please sign in to leave a comment.