Get details of a workflow run

This call returns detailed information about the specified workflow run.

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

Request

Example request

GET /ga4gh/wes/v1/runs/fc442b04-c8f5-4da1-aad3-26f9b4909e06 HTTP/1.1 Host: ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0
curl --location --request GET 'https://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/ga4gh/wes/v1/runs/fc442b04-c8f5-4da1-aad3-26f9b4909e06' \ --header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \

Header Fields

NameDescription
X-SBG-Auth-Token
required
Your authentication token.

Path parameters

NameDescription
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

NameData typeDescription
run_idstringWorkflow run ID
requestobject (RunRequest)Run request sent to execute the workflow.
statestring (State)Status of the running workflow
run_logobject (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_logsArray 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
outputsobjectThe outputs from the workflow run.

Example response body

{ "run_id": "0691458a-f02b-47c2-9f25-30a1510b82a8", "request": { "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", "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/0691458a-f02b-47c2-9f25-30a1510b82a8/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://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d50844f0c9f5f2f280e61", "stderr": "drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d50844f0c9f5f2f280e61", "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/b5c40295-4816-4334-a3ea-b99755ed951a/tasks/0691458a-f02b-47c2-9f25-30a1510b82a8/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://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d4e5c4f0c9f5f2f27d344", "stderr": "drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d4e5c4f0c9f5f2f27d344", "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://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d4c214f0c99ebf7eff9bf", "stderr": "drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d4c214f0c99ebf7eff9bf", "exit_code": 0 } ], "outputs": { "summary_metrics": { "path": "drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/5a9d50884f0c99ebf7efffdd", "size": 2125, "name": "HCC1143.merged.summary_metrics.txt", "class": "File" } } }