Get details of a workflow run

This call returns detailed information about the specified workflow run.

https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs/{run_id}

Request

Example request

GET /ga4gh/wes/v1/runs/5a4c3582-cbe1-5ba4-8945-af338969c510 HTTP/1.1
Host: cgc-ga4gh-api.sbgenomics.com
X-SBG-Auth-Token: 7eab0822exAMPle23d7d14c2eEXampLE
curl --location --request GET 'https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs/5a4c3582-cbe1-5ba4-8945-af338969c510' \
--header 'X-SBG-Auth-Token: 7eab0822exAMPle23d7d14c2eEXampLE' \

Header Fields

Name

Description

X-SBG-Auth-Token
required

Your authentication token.

Path parameters

Name

Description

run_id
required

The ID of the task you are querying

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

request

object (RunRequest)

Run request sent to execute the workflow.

state

string (State)

Status of the running workflow

run_log

object (Log)

Information about the task:

name - The task name

start_time- When the task started executing

end_time - When the task stopped executing (completed, failed, or cancelled)

exit_code - Exit code of the entire run

task_logs

Array of objects (Log)

The logs, and other key info like timing and exit code, for each step (job) in the workflow run.

name - The job name

start_time- When the command started executing

end_time - When the command stopped executing

stdout - A URL to retrieve standard output logs of the job

stderr - A URL to retrieve standard error logs of the job

exit_code - Exit code of the job

outputs

object

The outputs from the workflow run.

Example response body

{
  "run_id": "e3ed2ce1-8f8c-14a9-bd71-4cebd2ee441f",
  "request": {
    "workflow_params": {
      "project": "rfranklin/my-project",
      "inputs": {
        "input_list": [
          {
            "path": "drs://cgc-ga4gh-api.sbgenomics.com/567890abc9b0307bc0414164",
            "name": "C835.HCC1143.2.converted.realigned.base_recalibrated.bam",
            "class": "File"
          }
        ],
        "Reference_Genome_FASTA": {
          "path": "drs://cgc-ga4gh-api.sbgenomics.com/568e69abe9b0307bc0498765",
          "name": "Homo_sapiens_assembly38.fasta",
          "class": "File"
        }
      }
    },
    "workflow_type": "CWL",
    "workflow_type_version": "v1.0",
    "tags": {},
    "workflow_engine_params": {},
    "workflow_url": "sbg://rfranklin/my-project/alignment-metrics-qc/0"
  },
  "state": "COMPLETED",
  "run_log": {
    "name": "Alignment Metrics QC run - 03-05-18 13:41:03",
    "cmd": null,
    "start_time": "2020-03-05T13:51:33Z",
    "end_time": "2020-03-05T14:13:28Z",
    "stdout": null,
    "stderr": null,
    "exit_code": 0
  },
  "task_logs": [
    {
      "name": "alignment-metrics-qc_Picard_CollectAlignmentSummaryMetrics",
      "cmd": [
        "java -Xmx2048M -jar /opt/picard-tools-1.140/picard.jar CollectAlignmentSummaryMetrics INPUT=/sbgenomics/workspaces/b5c40295-4816-4334-a3ea-b99755ed951a/tasks/0151458a-f12b-43c2-9f25-30a1510b82a8/alignment-metrics-qc_Picard_MergeSamFiles/HCC1143.merged.bam OUTPUT=HCC1143.merged.summary_metrics.txt REFERENCE_SEQUENCE=/sbgenomics/Projects/b5c40295-4816-4334-a3ea-b99755ed951a/Homo_sapiens_assembly38.fasta VALIDATION_STRINGENCY=SILENT"
      ],
      "start_time": "2020-03-05T14:04:43Z",
      "end_time": "2020-03-05T14:13:26Z",
      "stdout": "drs://cgc-ga4gh-api.sbgenomics.com/567890abc9b0307bc0414164",
      "stderr": "drs://cgc-ga4gh-api.sbgenomics.com/567890abc9b0307bc0414164",
      "exit_code": 0
    },
    {
      "name": "alignment-metrics-qc_Picard_MergeSamFiles",
      "cmd": "java -Xmx2048M -jar /opt/picard-tools-1.140/picard.jar MergeSamFiles OUTPUT=HCC1143.merged.bam VALIDATION_STRINGENCY=SILENT INPUT=/sbgenomics/workspaces/b5c12345-0987-4334-a3ea-b11755ed951a/tasks/144a9a82-44b6-5d77-a35b-92b0429ecc38/alignment-metrics-qc_Picard_MergeSamFiles/C835.HCC1143.2.converted.realigned.base_recalibrated.bam",
      "start_time": "2020-03-05T13:55:22Z",
      "end_time": "2020-03-05T14:04:15Z",
      "stdout": "drs://cgc-ga4gh-api.sbgenomics.com/567890abc9b0307bc0414164",
      "stderr": "drs://cgc-ga4gh-api.sbgenomics.com/567890abc9b0307bc0414164",
      "exit_code": 0
    },
    {
      "name": "alignment-metrics-qc_SBG_FlattenLists",
      "cmd": "echo \"Output is now a single list\"",
      "start_time": "2020-03-05T13:54:30Z",
      "end_time": "2020-03-05T13:54:49Z",
      "stdout": "drs://cgc-ga4gh-api.sbgenomics.com/567890abc9b0307bc0414164",
      "stderr": "drs://cgc-ga4gh-api.sbgenomics.com/567890abc9b0307bc0414164",
      "exit_code": 0
    }
  ],
  "outputs": {
    "summary_metrics": {
      "path": "drs://cgc-ga4gh-api.sbgenomics.com/5a9d50123f0c99ebf7efffdd",
      "size": 2125,
      "name": "HCC1143.merged.summary_metrics.txt",
      "class": "File"
    }
  }
}

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