Bug #10327

arvados-cwl-runner fails to find secondaryFiles

Added by michael kotliar over 2 years ago. Updated over 1 year ago.

Status:
New
Priority:
Normal
Assigned To:
-
Category:
Crunch
Target version:
Start date:
10/21/2016
Due date:
% Done:

0%

Estimated time:
Story points:
-

Description

Hello. Following example always fails with error, no matter which way I set secondaryFiles. I assumed that this is a bug, because for cwl-runner (v1.0) it works fine. Both files (aligned.bam and aligned.bam.bai) are in the same folder.

    IOError: [Errno 2] File not found: u'aligned.bam.bai'

Testing example:
- task.cwl

cwlVersion: v1.0
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: ubuntu

requirements:
  - class: InlineJavascriptRequirement

baseCommand: echo
arguments:
  - valueFrom: $(inputs.fileName.basename)
    position: 1
  - valueFrom: $(inputs.fileName.secondaryFiles[0].basename)
    position: 2

inputs:
  fileName:
    type: File
#    secondaryFiles:
#      - .bai
    secondaryFiles: |
       ${
           return {"location": self.location+".bai", "class": "File"};
       }

outputs: []

- job.yml

{
    "fileName": {
        "class": "File",
        "location": "aligned.bam" 
    }
}

History

#1 Updated by Tom Morris over 1 year ago

  • Target version set to Arvados Future Sprints

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