Arvados

Using our WGS-processing tutorial workflow, you can run it as documented from the CWL file:

% arvados-cwl-runner --project-uuid=tordo-j7d0g-k2n54uzxzdl7gxp --name="chr19 run January 2025" --disable-reuse --no-wait --submit cwl/wgs-processing-wf.cwl  yml/wgs-processing-wf-chr19.yml
INFO /usr/bin/arvados-cwl-runner 3.1.0.dev20241209170209, arvados-python-client 3.1.0.dev20241209170209, cwltool 3.1.20240508115724
INFO Resolved 'cwl/wgs-processing-wf.cwl' to 'file:///home/brett/tutorial/WGS-processing/cwl/wgs-processing-wf.cwl'
INFO Git provenance
INFO   gitCommit: e4d896f5f94a9cf7b157cf87d5042e416649d87b
INFO   gitDate: Fri, 8 Nov 2024 13:57:48 -0500
INFO   gitCommitter: Peter Amstutz <peter.amstutz@curii.com>
INFO   gitBranch: main
INFO   gitOrigin: https://github.com/arvados/arvados-tutorial
INFO   gitDescribe: e4d896f
INFO   gitPath: /WGS-processing/cwl/wgs-processing-wf.cwl
INFO Using cluster tordo (https://workbench.tordo.arvadosapi.com/)
INFO Upload local files: "head.html" "generatereport.py" "tail.html" 
INFO Using collection 4fce132bc4ae9b4cc844115246a6bd41+175 (tordo-4zz18-bhcbk71jya1ua5m)
INFO Uploading workflow dependencies
INFO Workflow uploaded to tordo-4zz18-39oncy07f9az1vx
INFO Using collection cache size 256 MiB
INFO [container chr19 run January 2025] submitted container_request tordo-xvhdp-hr5370pocazfy67
INFO Monitor workflow progress at https://workbench.tordo.arvadosapi.com/processes/tordo-xvhdp-hr5370pocazfy67
tordo-xvhdp-hr5370pocazfy67
INFO Final process status is success

But if you register the workflow, then try to run that, it will fail because it can't validate that the inputs have the right format:

% arvados-cwl-runner --update-workflow tordo-7fd4e-gt18h1279e2wawq cwl/wgs-processing-wf.cwl
INFO /usr/bin/arvados-cwl-runner 3.1.0.dev20241209170209, arvados-python-client 3.1.0.dev20241209170209, cwltool 3.1.20240508115724
INFO Resolved 'cwl/wgs-processing-wf.cwl' to 'file:///home/brett/tutorial/WGS-processing/cwl/wgs-processing-wf.cwl'
INFO Git provenance
INFO   gitCommit: e4d896f5f94a9cf7b157cf87d5042e416649d87b
INFO   gitDate: Fri, 8 Nov 2024 13:57:48 -0500
INFO   gitCommitter: Peter Amstutz <peter.amstutz@curii.com>
INFO   gitBranch: main
INFO   gitOrigin: https://github.com/arvados/arvados-tutorial
INFO   gitDescribe: e4d896f
INFO   gitPath: /WGS-processing/cwl/wgs-processing-wf.cwl
INFO Using cluster tordo (https://workbench.tordo.arvadosapi.com/)
INFO Uploading workflow dependencies
[Docker image upload logs omitted]
2025-01-13 15:28:37 arvados.cwl-runner[1702876] INFO: Workflow uploaded to tordo-4zz18-39oncy07f9az1vx
tordo-7fd4e-gt18h1279e2wawq
2025-01-13 15:28:39 cwltool[1702876] INFO: Final process status is success

% arvados-cwl-runner --project-uuid=tordo-j7d0g-k2n54uzxzdl7gxp --name="chr19 run January 2025" --disable-reuse --no-wait --submit tordo-7fd4e-gt18h1279e2wawq yml/wgs-processing-wf-chr19.yml
INFO /usr/bin/arvados-cwl-runner 3.1.0.dev20241209170209, arvados-python-client 3.1.0.dev20241209170209, cwltool 3.1.20240508115724
INFO Resolved 'tordo-7fd4e-gt18h1279e2wawq' to 'arvwf:tordo-7fd4e-gt18h1279e2wawq#main'
INFO Git provenance
INFO   gitCommit: e4d896f5f94a9cf7b157cf87d5042e416649d87b
INFO   gitDate: Fri, 8 Nov 2024 13:57:48 -0500
INFO   gitCommitter: Peter Amstutz <peter.amstutz@curii.com>
INFO   gitBranch: main
INFO   gitOrigin: https://github.com/arvados/arvados-tutorial
INFO   gitDescribe: e4d896f
INFO   gitPath: /WGS-processing/cwl/wgs-processing-wf.cwl
INFO Using cluster tordo (https://workbench.tordo.arvadosapi.com/)
INFO Upload local files: "tail.html" "head.html" "generatereport.py" 
INFO Using collection 4fce132bc4ae9b4cc844115246a6bd41+175 (tordo-4zz18-bhcbk71jya1ua5m)
INFO Using collection cache size 256 MiB
ERROR Workflow error, try again with --debug for more information:
Expected value of 'clinvarvcf' to have format 'http://edamontology.org/format_3016' but
 File has an incompatible format: {
    "class": "File",
    "format": "edam:format_3016",
    "location": "keep:18657d75efb4afd31a14bb204d073239+13611/clinvar.vcf.gz",
    "size": 25161134,
    "basename": "clinvar.vcf.gz",
    "nameroot": "clinvar.vcf",
    "nameext": ".gz" 
}