Bug #9674

[CWL] InitialWorkDirRequirement not working as expected

Added by Bryan Cosca over 3 years ago. Updated over 3 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
07/27/2016
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
0.5

Description

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
baseCommand: []
requirements:
  InlineJavascriptRequirement: {}
  InitialWorkDirRequirement:
    listing:
      - $(inputs.inputsam)
inputs:
  splitSamIntoChrom:
    type: File
    inputBinding:
      position: 0
  chr-chrom-lst:
    type: File
    inputBinding:
      position: 1
  inputsam:
    type: File
    inputBinding:
      position: 2
      valueFrom: $(self.basename)
outputs:
  output-sam:
    type:
      type: array
      items: File
    outputBinding:
      glob: "*sam" 
arvados-cwl-runner --local splitsam-test.cwl splitsam-test.json 
/usr/local/bin/arvados-cwl-runner 1.0.20160713211920, arvados-python-client 0.1.20160713191718, cwltool 1.0.20160712154127
2016-07-27 19:11:13 arvados.cwl-runner[64747] INFO: Pipeline instance qr1hi-d1hrv-2fb0mcilpm2ehpf
2016-07-27 19:11:14 arvados.arv-run[64747] INFO: Upload local files: "splitSamIntoChrom.pl" "chr_chrom.lst" 
2016-07-27 19:11:14 arvados.arv-run[64747] INFO: Using collection qr1hi-4zz18-gow6notm9tzd0wa
2016-07-27 19:11:20 arvados.cwl-runner[64747] ERROR: Caught unhandled exception, marking pipeline as failed.  Error was: [Errno 2] No such file or directory: '$(task.outdir)/keep:c00bea363a0770335e81662bb7980051+269668/sample.sam'
Workflow error, try again with --debug for more information:
  Workflow did not return a result.
{
  "splitSamIntoChrom":{
        "class":"File",
        "path":"splitSamIntoChrom.pl" 
  },
  "chr-chrom-lst":{
        "class":"File",
        "path":"chr_chrom.lst" 
  },
  "inputsam":{
        "class":"File",
        "path":"keep:c00bea363a0770335e81662bb7980051+269668/sample.sam" 
  }
}

Subtasks

Task #9708: Review 9674-cwl-initialworkdirResolvedPeter Amstutz


Related issues

Related to Arvados - Story #9397: [Crunch2] Support prepopulating the output directory - CWL InitialWorkDirRequirementResolved01/31/2017

Associated revisions

Revision 5bf34f18
Added by Peter Amstutz over 3 years ago

Merge branch '9674-cwl-initialworkdir' closes #9674

History

#1 Updated by Bryan Cosca over 3 years ago

  • Description updated (diff)

#2 Updated by Peter Amstutz over 3 years ago

  • Status changed from New to In Progress
  • Assigned To set to Peter Amstutz

#3 Updated by Peter Amstutz over 3 years ago

Branch @ 9674-cwl-initialworkdir

#4 Updated by Bryan Cosca over 3 years ago

The test seems to be running fine here: https://cloud.curoverse.com/jobs/qr1hi-8i9sb-hmd0rupxce270am#Status

Its a bigger sample, so it might not finish, but it got through the part where it errored out last time.

#5 Updated by Peter Amstutz over 3 years ago

  • Target version set to 2016-08-17 sprint

#6 Updated by Radhika Chippada over 3 years ago

  • Story points set to 0.5

#7 Updated by Tom Clegg over 3 years ago

9674-cwl-initialworkdir LGTM

#8 Updated by Peter Amstutz over 3 years ago

  • Status changed from In Progress to Resolved
  • % Done changed from 0 to 100

Applied in changeset arvados|commit:5bf34f18516d25f252881f4bbf01f4fe7cd14535.

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