Bug #10308

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

Added by michael kotliar over 2 years ago. Updated over 2 years ago.

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

0%

Estimated time:
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

History

#1 Updated by michael kotliar over 2 years ago

Works fine with

glob: "." 

#2 Updated by Tom Morris over 2 years ago

  • Subject changed from Set glob to return Directory as output form cwl workflow to Output glob "./" doesn't work as output from CWL workflow
  • Target version set to Arvados Future Sprints

Since both forms ("./" and ".") are equivalent, it seems like they should both be supported.

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