This addresses issue #711 by parsing the workflow after moving the wf cwl directory to a tmp directory and copying the alternate files in then packaging and parsing the new package. Previously, the workflow was parsed directly from the workflow path before copying the alternate files.
This addresses issue #711 by parsing the workflow after moving the wf cwl directory to a tmp directory and copying the alternate files in then packaging and parsing the new package. Previously, the workflow was parsed directly from the workflow path before copying the alternate files.