Bug #16339

Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl errors

Added by Michael Crusoe 11 months ago. Updated 7 months ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Peter Amstutz
Category:
CWL
Target version:
2020-08-12 Sprint
Start date:
Due date:
% Done:

0%

Estimated time:
Story points:
-
Release:
Arvados 2.0.3
Release relationship:
Auto

Description

$ arvados-cwl-runner Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl Ambarish_Kumar_SOP-GATK-SAR-CoV-2_inputs.yml   
INFO /home/michael/src/2020-covid-19-bh/env3.7/bin/arvados-cwl-runner 2.0.1, arvados-python-client 2.0.1, cwltool 1.0.20190831161204
INFO Resolved 'Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl' to 'file:///home/michael/src/2020-covid-19-bh/Ambarish_Kumar_SOP/Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl'
WARNING Workflow checker warning:
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:57:12: Source 'sequences_with_dictionary' of type "File" may
                                             be incompatible
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:88:7:    with sink 'reference' of type "File" 
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:57:12: Source 'sequences_with_dictionary' of type "File" may
                                             be incompatible
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl:105:7:   with sink 'reference' of type "File" 
INFO Upload local files: "ebola_mut_reads1.fq" "ebola_mut_reads2.fq" "ebola_ref.fasta" 
INFO Using collection bcb759e2e40dcd91eedcded863913a7c+219 (lugli-4zz18-kk9c9rhbzq5wf4s)
INFO Downloading http://edamontology.org/EDAM_1.18.owl (2752312 bytes)
ERROR Unhandled error, try again with --debug for more information:
  <HttpError 422 when requesting https://lugli.arvadosapi.com/arvados/v1/collections?ensure_unique_name=true&alt=json returned "request failed: http://localhost:8004/arvados/v1/collections: 422 Unprocessable Entity: Name cannot contain a '/' character (req-8gddg6hazk0npc8pvpt2)">

Associated revisions

Revision 5c222ee2
Added by Peter Amstutz 10 months ago

Merge branch '16339-cwl-schema-refs' refs #16339

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <>

History

#1 Updated by Peter Amstutz 10 months ago

  • Target version set to 2020-05-20 Sprint

#2 Updated by Peter Amstutz 10 months ago

  • Target version changed from 2020-05-20 Sprint to 2020-06-03 Sprint

#3 Updated by Peter Amstutz 10 months ago

  • Release set to 33

#4 Updated by Peter Amstutz 10 months ago

  • Status changed from New to In Progress

#5 Updated by Peter Amstutz 10 months ago

  • Target version changed from 2020-06-03 Sprint to 2020-06-17 Sprint

#6 Updated by Peter Amstutz 9 months ago

  • Target version changed from 2020-06-17 Sprint to 2020-07-01 Sprint

#7 Updated by Peter Amstutz 9 months ago

  • Assigned To set to Peter Amstutz

#8 Updated by Peter Amstutz 9 months ago

  • Category set to CWL

#9 Updated by Peter Amstutz 8 months ago

  • Target version changed from 2020-07-01 Sprint to 2020-07-15

#10 Updated by Peter Amstutz 8 months ago

  • Target version changed from 2020-07-15 to 2020-08-12 Sprint

#11 Updated by Peter Amstutz 7 months ago

  • Status changed from In Progress to Resolved

One fix for $schemas was committed.

When I dug into the workflow previously, I found errors in the workflow itself that were not Arvados issues. Not planning on following up at this time, marking as resolved.

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