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

Error with --outdir

Offen
#205 7 Kommentare 0 Reaktionen 0 zugewiesene Personen Auf GitHub ansehen
Vorherrschende Sprache
Python
Sterne
376
Forks
255
Ø Merge
2 T. 7 Std.
Gemergte PRs (30 T.)
12

Beschreibung

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.

Beitragsleitfaden

Beitragsleitfaden öffnen

Bewertung

Dieses Issue wurde noch nicht bewertet.

Neue Issues direkt in Ihr Postfach

Eine kurze Übersicht über anfängerfreundliche GitHub-Issues.