common-workflow-language / common-workflow-language/cwltool

Error with --outdir

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Description

When I run the command:

cwltool --cachedir workflow_cache --outdir workflow_output completeWorkflow.cwl input.yml

I get:

Unhandled error, try again with --debug for more information:
[Errno 2] No such file or directory: ''

Here's what I get with --debug:

Unhandled error, try again with --debug for more information:
[Errno 2] No such file or directory: ''
Traceback (most recent call last):
File "/home/mepstein/.local/lib/python2.7/site-packages/cwltool/main.py", line 721, in main
**vars(args))
File "/home/mepstein/.local/lib/python2.7/site-packages/cwltool/main.py", line 230, in single_job_executor
output_dirs, kwargs.get("move_outputs"))
File "/home/mepstein/.local/lib/python2.7/site-packages/cwltool/process.py", line 215, in relocateOutputs
stageFiles(pm, moveIt)
File "/home/mepstein/.local/lib/python2.7/site-packages/cwltool/process.py", line 176, in stageFiles
os.makedirs(os.path.dirname(p.target), 0755)
File "/usr/lib/python2.7/os.py", line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 2] No such file or directory: ''

When I add some debugging print's to process.py, I see (just before the error):

MapperEnt(resolved='file:///home/mepstein/tmp/workflows/workflow_cache/9540f1f896b3ab1f435e83798bcf79f5', target='workflow_output', type='Directory')

so when it does os.path.dirname() on 'workflow_output', it's '', hence the error.

Is this a bug in cwltool?

Note that when I run the same command without --outdir, or I do a command like:

cwltool --cachedir /shared/mepstein/cachedir --outdir /shared/mepstein/workflow_output completeWorkflow.cwl input.yml

it works fine, there's no error.

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