Bug #16339
Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl errors
Start date:
Due date:
% Done:
0%
Estimated time:
Story points:
-
Release:
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
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.
Merge branch '16339-cwl-schema-refs' refs #16339
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>