I have the following workflow (take geometry, create orbiting camera, render image sequence, create movie from sequence)
My renderScene step depends on output from both step “orbitCamera” and “blenderScene” but when the renderScene step runs, the output from orbitCamera has already been cleared.
I know there are flags in cwl-runner to keep all the tmp files and such but I was hoping that the dependency should tell cwl-runner to keep things around or have I misunderstood the nature of input/output dependencies in CWL ?
Yes, it is absolutely supposed to preserve files between steps. Maybe you are not capturing the outputs properly? Perhaps you could paste the code from your “orbitCamera” tools.
Separately, this is incorrect at the Workflow level:
You need to connect the output from the renderScene step instead:
cwl-runner is the generic name, it could be any runner. You might be using cwltool already, just as a different name. What does it say if you do cwl-runner --version ?