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lilab-bcb / altocumulus

Command line tool for submitting WDL jobs to Terra or Cromwell server.
https://altocumulus.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Auto workflow dependency fails in some cases #40

Open yihming opened 2 years ago

yihming commented 2 years ago

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.