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Bug #10308

closed

Output glob "./" doesn't work as output from CWL workflow

Added by michael kotliar about 8 years ago. Updated over 3 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
Crunch
Start date:
10/20/2016
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
-

Description

Hello! Found a problem while trying return directory from cwl. Tested the following cwl on both cwl-runner and arvados-cwl-runner. According to documentation both support cwl v1.0. On cwl-runner all works fine: receive file according to the parameter set in $(inputs.fileName).
When trying to run the same cwl with arvados-cwl-runner get an error:
WorkflowException: Error collecting output for parameter 'dir': Did not find output file with glob pattern: '['./']'

Example that I tested

task.cwl

cwlVersion: v1.0
class: CommandLineTool
hints:
  DockerRequirement:
    dockerPull: ubuntu
baseCommand: echo
arguments: ["return dir"]
requirements:
  InitialWorkDirRequirement:
    listing:
      - entryname: $(inputs.fileName)
        entry: Some text inside the file

inputs:
  fileName:
    type: string

outputs:
  dir:
    type: Directory
    outputBinding:
      glob: "./" 

job.yml
fileName: textfile.txt


Subtasks 1 (0 open1 closed)

Task #17558: Review 17521-dot-slash-globResolvedPeter Amstutz10/20/2016

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Related issues 1 (0 open1 closed)

Related to Arvados - Bug #17521: Handling of ./ in arvados-cwl-runnerResolvedPeter Amstutz

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