Auto workflow dependency fails in some cases

[yihming]

Issue Details

The current workflow dependency zip file creation feature fails for the following case.

If calling https://github.com/lilab-bcb/cumulus/blob/master/workflows/cellranger/cellranger_workflow.wdl locally:

alto cromwell run -m <server-name> -m cellranger_workflow.wdl -i inputs.json -b <Cloud-bucket-URI>

The job fails with the following error:

Failed to import '../cumulus/cumulus_adt.wdl' (reason 2 of 2): Failed to resolve '../cumulus/cumulus_adt.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path

Solution Suggestion

Dockstore handles WDL import statements on relative paths with .. properly. Maybe we can borrow some idea there?

Urgency Level

Not urgent at all.