Run a workflow

This call runs (executes) a workflow and returns the run ID which you can use to monitor its progress (see Get details of a workflow run).

https://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/ga4gh/wes/v1/runs

Request

Example request

POST /ga4gh/wes/v1/runs HTTP/1.1
Host: ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov
X-SBG-Auth-Token: 55e9691c111146bd384c5ec40a9f97fb1

curl --location --request POST 'https://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/ga4gh/wes/v1/runs' \
--header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \
--header 'Cookie: language=en' \
--form 'workflow_params={"project": "rfranklin/my-project", "use_interruptible_instances": true, "inputs": {"input_bam": {"class": "File", "path": "drs://cavatica-ga4gh-api.sbgenomics.com/5f7b09a2e4b0e67085ff9386"}}};type=application/json'  \
--form 'workflow_type=CWL' \
--form 'tags={}' \
--form 'workflow_engine_parameters={}' \
--form 'workflow_url=sbg://rfranklin/my-project/tool/0'

Header Fields

Name	Description
`X-SBG-Auth-Token` required	Your authentication token.

Request body

📘
When running new workflow via WES on the BiodataCatalyst powered by Seven Bridges, you need to specify the target project via the project parameter. See below.

Name	Data type	Description
`workflow_params` required	object	Specify the name of the project using the `project` (required) parameter , e.g. `"project": "rfranklin/my-project"`. You can also use this parameter to specify the input files: The path to the files can be specified either as a platform-local DRS URI or file ID. Option to specify files via an external DRS URI is coming soon.
`workflow_type` required	string	The type of workflow language submitted which is supported by this WES instance.
`workflow_type_version` required	string	The version of the workflow language submitted which is supported by this WES instance.
`tags`	string	Specify tags.
`workflow_url` required	string	This parameter is used for specifying the location of the App, which can be any of the following: App in your project - specify the URL to the app, e.g. `sbg://admin/sbg-public-data/topmed-alignment` App in the Dockstore - specify the URL to your app in the Dockstore, using the standard HTTP or TRS format * App uploaded via `workflow_attachment` - specify the relative path to the appropriate attachment, e.g. `#/workflow_attachment/0`
`workflow_attachment`	Array of strings	The `workflow_attachment` array may be used to upload the App needed to execute the workflow.

Example request body

{
  "workflow_params": {
    "project": "rfranklin/my-project",
    "inputs": {
      "input_list": [
        {
          "path": "drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d49c04f0c482419bb5f8e",
          "name": "C835.HCC1143.2.converted.realigned.base_recalibrated.bam",
          "class": "File"
        }
      ],
      "Reference_Genome_FASTA": {
        "path": "drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d49d54f0c482419bb5f98",
        "name": "Homo_sapiens_assembly38.fasta",
        "class": "File"
      }
    }
  },
  "workflow_type": "CWL",
  "workflow_type_version": "v1.0",
  "workflow_url": "sbg://rfranklin/my-project/alignment-metrics-qc/0"
}

Response

See a list of response codes that may be contained in the body of the response.

Response body

Name	Data type	Description
`run_id`	string	Workflow run ID

Example response body

{
  "run_id": "103e7bc8-224e-4c97-9664-6f98a2cb7e2d"
}