Workflow Type: Common Workflow Language
Work-in-progress

rquest-omop-worker-workflows

Source for workflow definitions for the open source RQuest OMOP Worker tool developed for Hutch/TRE-FX

Note: ARM workflows are currently broken. x86 ones work.

Inputs

### Body Sample input payload:

{
  "task_id": "job-2023-01-13-14: 20: 38-",
  "project": "",
  "owner": "",
  "cohort": {
    "groups": [
      {
        "rules": [
          {
            "varname": "OMOP",
            "varcat": "Person",
            "type": "TEXT",
            "oper": "=",
            "value": "8507"
          }
        ],
        "rules_oper": "AND"
      }
    ],
    "groups_oper": "OR"
  },
  "collection": "",
  "protocol_version": "",
  "char_salt": "",
  "uuid": ""
}

Database access

Currently this workflow requires inputs for connecting to the database it will run queries against.

In future this may be moved to environment variables.

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Inputs

ID Name Description Type
body n/a n/a
  • File
result_modifiers n/a n/a
  • string?
is_availability n/a n/a
  • boolean
results n/a n/a
  • string?

Steps

ID Name Description
run_query n/a n/a

Outputs

ID Name Description Type
output_file n/a n/a
  • File

Version History

main @ 724775a (latest) Created 23rd Oct 2023 at 14:58 by Vasiliki Panagi

Merge pull request #1 from HDRUK/env_variables

Remove db parameters from workflows


Frozen main 724775a

main @ 8a4c8c1 Created 10th Oct 2023 at 16:03 by Jon Couldridge

adding cwl files


Frozen main 8a4c8c1

main @ b916ecf (earliest) Created 15th May 2023 at 17:15 by Stian Soiland-Reyes

AB105814: Create scope in HostedService for WfexsJobService (#194)


Frozen main b916ecf
help Creators and Submitter
Creator
Submitter
Citation
Panagi, V. (2024). rquest-omop-worker-workflow. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.471.3
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Views: 3041   Downloads: 1119

Created: 15th May 2023 at 17:15

Last updated: 23rd Oct 2023 at 14:58

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