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broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
http://cromwell.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Changing directories in the command block causes workflow failure #3116

Open jonn-smith opened 6 years ago

jonn-smith commented 6 years ago

Running the cd command anywhere in the command block causes output files to not be found and for the workflow to throw an error:

[2018-01-08 15:05:21,44] [error] WorkflowManagerActor Workflow 6575132f-3c01-498f-ac7a-2a418568f002 failed (during ExecutingWorkflowState): Could not process output, file not found: /Users/jonn/Development/cromwell/cromwell-executions/Funcotator/6575132f-3c01-498f-ac7a-2a418568f002/call-MakeItFunky/execution/out.vcf

geoffjentry commented 5 years ago

Yeah, that makes sense.

Note to future implementer - it seems like it'd work to capture pwd prior to starting the user's command and then forcibly reverting to that directory prior to delocalizaiton & such