{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","settings":"","results":{"codes":[]},"params":[]},"next":{"description":"","pages":[]},"title":"Get details of a workflow run","type":"basic","slug":"get-details-of-a-workflow-run","excerpt":"","body":"This call returns detailed information about the specified workflow run.\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs/{run_id}\",\n      \"language\": \"text\",\n      \"name\": \"Path\"\n    }\n  ]\n}\n[/block]\n##Request\n\n###Example request\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"GET /ga4gh/wes/v1/runs/fc442b04-c8f5-4da1-aad3-26f9b4909e06 HTTP/1.1\\nHost: cgc-ga4gh-api.sbgenomics.com\\nX-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0\\n\",\n      \"language\": \"http\",\n      \"name\": null\n    },\n    {\n      \"code\": \"curl --location --request GET 'https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs/fc442b04-c8f5-4da1-aad3-26f9b4909e06' \\\\\\n--header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \\\\\",\n      \"language\": \"curl\",\n      \"name\": \"cURL\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]\n\n###Header Fields\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"`X-SBG-Auth-Token`\\n*required*\",\n    \"0-1\": \"Your [authentication token](doc:get-your-authentication-token).\",\n    \"h-2\": \"\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n\n###Path parameters\n[block:parameters]\n{\n  \"data\": {\n    \"0-0\": \"`run_id`\\n*required*\",\n    \"h-0\": \"Name\",\n    \"h-1\": \"Description\",\n    \"0-1\": \"The ID of the task you are querying\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n##Response\n\n[See a list of response codes that may be contained in the body of the response.](doc:api-status-codes) \n\n###Response body\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"Data type\",\n    \"h-2\": \"Description\",\n    \"0-0\": \"`run_id`\",\n    \"1-0\": \"`request`\",\n    \"2-0\": \"`state`\",\n    \"3-0\": \"`run_log`\",\n    \"4-0\": \"`task_logs`\",\n    \"5-0\": \"`outputs`\",\n    \"0-1\": \"string\",\n    \"1-1\": \"object ([RunRequest](doc:run-a-workflow#section-request-body))\",\n    \"2-1\": \"string ([State](doc:get-the-status-of-the-workflow-run#section-response))\",\n    \"3-1\": \"object (Log)\",\n    \"4-1\": \"Array of objects (Log)\",\n    \"5-1\": \"object\",\n    \"0-2\": \"Workflow run ID\",\n    \"1-2\": \"Run request sent to execute the workflow.\",\n    \"2-2\": \"Status of the running workflow\",\n    \"3-2\": \"Information about the task:\\n\\n`name` - The task name\\n\\n`start_time`- When the task started executing\\n\\n`end_time` - When the task stopped executing (completed, failed, or cancelled)\\n\\n`exit_code` - Exit code of the entire run\",\n    \"4-2\": \"The logs, and other key info like timing and exit code, for each step (job) in the workflow run.\\n\\n`name` - The job name\\n\\n`start_time`- When the command started executing\\n\\n`end_time` - When the command stopped executing\\n\\n`stdout` - A URL to retrieve standard output logs of the job\\n\\n`stderr` - A URL to retrieve standard error logs of the job\\n\\n`exit_code` - Exit code of the job\",\n    \"5-2\": \"The outputs from the workflow run.\"\n  },\n  \"cols\": 3,\n  \"rows\": 6\n}\n[/block]\n###Example response body\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"run_id\\\": \\\"0691458a-f02b-47c2-9f25-30a1510b82a8\\\",\\n  \\\"request\\\": {\\n    \\\"workflow_params\\\": {\\n      \\\"project\\\": \\\"rfranklin/my-project\\\",\\n      \\\"inputs\\\": {\\n        \\\"input_list\\\": [\\n          {\\n            \\\"path\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d49c04f0c482419bb5f8e\\\",\\n            \\\"name\\\": \\\"C835.HCC1143.2.converted.realigned.base_recalibrated.bam\\\",\\n            \\\"class\\\": \\\"File\\\"\\n          }\\n        ],\\n        \\\"Reference_Genome_FASTA\\\": {\\n          \\\"path\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d49d54f0c482419bb5f98\\\",\\n          \\\"name\\\": \\\"Homo_sapiens_assembly38.fasta\\\",\\n          \\\"class\\\": \\\"File\\\"\\n        }\\n      }\\n    },\\n    \\\"workflow_type\\\": \\\"CWL\\\",\\n    \\\"workflow_type_version\\\": \\\"v1.0\\\",\\n    \\\"tags\\\": {},\\n    \\\"workflow_engine_params\\\": {},\\n    \\\"workflow_url\\\": \\\"sbg://rfranklin/my-project/alignment-metrics-qc/0\\\"\\n  },\\n  \\\"state\\\": \\\"COMPLETED\\\",\\n  \\\"run_log\\\": {\\n    \\\"name\\\": \\\"Alignment Metrics QC run - 03-05-18 13:41:03\\\",\\n    \\\"cmd\\\": null,\\n    \\\"start_time\\\": \\\"2020-03-05T13:51:33Z\\\",\\n    \\\"end_time\\\": \\\"2020-03-05T14:13:28Z\\\",\\n    \\\"stdout\\\": null,\\n    \\\"stderr\\\": null,\\n    \\\"exit_code\\\": 0\\n  },\\n  \\\"task_logs\\\": [\\n    {\\n      \\\"name\\\": \\\"alignment-metrics-qc_Picard_CollectAlignmentSummaryMetrics\\\",\\n      \\\"cmd\\\": [\\n        \\\"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\\\"\\n      ],\\n      \\\"start_time\\\": \\\"2020-03-05T14:04:43Z\\\",\\n      \\\"end_time\\\": \\\"2020-03-05T14:13:26Z\\\",\\n      \\\"stdout\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d50844f0c9f5f2f280e61\\\",\\n      \\\"stderr\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d50844f0c9f5f2f280e61\\\",\\n      \\\"exit_code\\\": 0\\n    },\\n    {\\n      \\\"name\\\": \\\"alignment-metrics-qc_Picard_MergeSamFiles\\\",\\n      \\\"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\\\",\\n      \\\"start_time\\\": \\\"2020-03-05T13:55:22Z\\\",\\n      \\\"end_time\\\": \\\"2020-03-05T14:04:15Z\\\",\\n      \\\"stdout\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4e5c4f0c9f5f2f27d344\\\",\\n      \\\"stderr\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4e5c4f0c9f5f2f27d344\\\",\\n      \\\"exit_code\\\": 0\\n    },\\n    {\\n      \\\"name\\\": \\\"alignment-metrics-qc_SBG_FlattenLists\\\",\\n      \\\"cmd\\\": \\\"echo \\\\\\\"Output is now a single list\\\\\\\"\\\",\\n      \\\"start_time\\\": \\\"2020-03-05T13:54:30Z\\\",\\n      \\\"end_time\\\": \\\"2020-03-05T13:54:49Z\\\",\\n      \\\"stdout\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\\\",\\n      \\\"stderr\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\\\",\\n      \\\"exit_code\\\": 0\\n    }\\n  ],\\n  \\\"outputs\\\": {\\n    \\\"summary_metrics\\\": {\\n      \\\"path\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5a9d50884f0c99ebf7efffdd\\\",\\n      \\\"size\\\": 2125,\\n      \\\"name\\\": \\\"HCC1143.merged.summary_metrics.txt\\\",\\n      \\\"class\\\": \\\"File\\\"\\n    }\\n  }\\n}\",\n      \"language\": \"json\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]","updates":[],"order":4,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"5f8950b84649f900680714f6","createdAt":"2020-10-16T07:50:16.868Z","user":"566590c83889610d0008a253","category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"WES API","slug":"wes-api","order":40,"from_sync":false,"reference":false,"_id":"5f894c7d3b0894006477ca01","createdAt":"2020-10-16T07:32:13.051Z","version":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":0},"version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":true,"is_hidden":false,"is_deprecated":false,"categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f","5c222bed4bc358002f21459a","5c22412594a2a5005cc9e919","5c41ae1c33592700190a291e","5c8a525e2ba7b2003f9b153c","5cbf14d58c79c700ef2b502e","5db6f03a6e187c006f667fa4","5f894c7d3b0894006477ca01","6176d5bf8f59c6001038c2f7"],"_id":"55faf11ba62ba1170021a9aa","releaseDate":"2015-09-17T16:58:03.490Z","createdAt":"2015-09-17T16:58:03.490Z","project":"55faf11ba62ba1170021a9a7","__v":48},"project":"55faf11ba62ba1170021a9a7","__v":0,"parentDoc":null}

GET STARTED

TUTORIALS

GUIDES

ACCESS THE CGC

MANAGE AN ANALYSIS ENVIRONMENT

COLLABORATE SECURELY

DATASETS HUB

PUBLIC PROJECTS

BRING DATA TO THE CGC

SET METADATA ASSOCIATED WITH A PRIVATE FILE

SEARCH FILES

ADD FILES TO A PROJECT

ORGANIZE FILES

ARCHIVE FILES

FIND APPS

BRING YOUR TOOLS

DOCKER

DESCRIBE YOUR TOOL (LEGACY)

TOOL WRAPPING TIPS AND TRICKS

EDIT AN APP (LEGACY)

ARCHIVE APPS

RUN AN ANALYSIS

TASK EXECUTION

REVIEW A TASK

VIEW ANALYSIS RESULTS

INTERACTIVE ANALYSIS

DOWNLOAD RESULTS

DEVELOPER TOOLS

CONNECT CLOUD STORAGE

API Hub

API CLIENTS

SB Command Line Interface

API Reference

EDIT AN APP

BULK API ACTIONS

ASYNC BULK ACTIONS

DRS API

WES API

DATA CRUNCHER

SBFS (Beta)

SBFS Command Reference

Get details of a workflow run

This call returns detailed information about the specified workflow run. [block:code] { "codes": [ { "code": "https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs/{run_id}", "language": "text", "name": "Path" } ] } [/block] ##Request ###Example request [block:code] { "codes": [ { "code": "GET /ga4gh/wes/v1/runs/fc442b04-c8f5-4da1-aad3-26f9b4909e06 HTTP/1.1\nHost: cgc-ga4gh-api.sbgenomics.com\nX-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0\n", "language": "http", "name": null }, { "code": "curl --location --request GET 'https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs/fc442b04-c8f5-4da1-aad3-26f9b4909e06' \\\n--header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \\", "language": "curl", "name": "cURL" } ], "sidebar": true } [/block] ###Header Fields [block:parameters] { "data": { "h-0": "Name", "h-1": "Description", "0-0": "`X-SBG-Auth-Token`\n*required*", "0-1": "Your [authentication token](doc:get-your-authentication-token).", "h-2": "" }, "cols": 2, "rows": 1 } [/block] ###Path parameters [block:parameters] { "data": { "0-0": "`run_id`\n*required*", "h-0": "Name", "h-1": "Description", "0-1": "The ID of the task you are querying" }, "cols": 2, "rows": 1 } [/block] ##Response [See a list of response codes that may be contained in the body of the response.](doc:api-status-codes) ###Response body [block:parameters] { "data": { "h-0": "Name", "h-1": "Data type", "h-2": "Description", "0-0": "`run_id`", "1-0": "`request`", "2-0": "`state`", "3-0": "`run_log`", "4-0": "`task_logs`", "5-0": "`outputs`", "0-1": "string", "1-1": "object ([RunRequest](doc:run-a-workflow#section-request-body))", "2-1": "string ([State](doc:get-the-status-of-the-workflow-run#section-response))", "3-1": "object (Log)", "4-1": "Array of objects (Log)", "5-1": "object", "0-2": "Workflow run ID", "1-2": "Run request sent to execute the workflow.", "2-2": "Status of the running workflow", "3-2": "Information about the task:\n\n`name` - The task name\n\n`start_time`- When the task started executing\n\n`end_time` - When the task stopped executing (completed, failed, or cancelled)\n\n`exit_code` - Exit code of the entire run", "4-2": "The logs, and other key info like timing and exit code, for each step (job) in the workflow run.\n\n`name` - The job name\n\n`start_time`- When the command started executing\n\n`end_time` - When the command stopped executing\n\n`stdout` - A URL to retrieve standard output logs of the job\n\n`stderr` - A URL to retrieve standard error logs of the job\n\n`exit_code` - Exit code of the job", "5-2": "The outputs from the workflow run." }, "cols": 3, "rows": 6 } [/block] ###Example response body [block:code] { "codes": [ { "code": "{\n \"run_id\": \"0691458a-f02b-47c2-9f25-30a1510b82a8\",\n \"request\": {\n \"workflow_params\": {\n \"project\": \"rfranklin/my-project\",\n \"inputs\": {\n \"input_list\": [\n {\n \"path\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d49c04f0c482419bb5f8e\",\n \"name\": \"C835.HCC1143.2.converted.realigned.base_recalibrated.bam\",\n \"class\": \"File\"\n }\n ],\n \"Reference_Genome_FASTA\": {\n \"path\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d49d54f0c482419bb5f98\",\n \"name\": \"Homo_sapiens_assembly38.fasta\",\n \"class\": \"File\"\n }\n }\n },\n \"workflow_type\": \"CWL\",\n \"workflow_type_version\": \"v1.0\",\n \"tags\": {},\n \"workflow_engine_params\": {},\n \"workflow_url\": \"sbg://rfranklin/my-project/alignment-metrics-qc/0\"\n },\n \"state\": \"COMPLETED\",\n \"run_log\": {\n \"name\": \"Alignment Metrics QC run - 03-05-18 13:41:03\",\n \"cmd\": null,\n \"start_time\": \"2020-03-05T13:51:33Z\",\n \"end_time\": \"2020-03-05T14:13:28Z\",\n \"stdout\": null,\n \"stderr\": null,\n \"exit_code\": 0\n },\n \"task_logs\": [\n {\n \"name\": \"alignment-metrics-qc_Picard_CollectAlignmentSummaryMetrics\",\n \"cmd\": [\n \"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\"\n ],\n \"start_time\": \"2020-03-05T14:04:43Z\",\n \"end_time\": \"2020-03-05T14:13:26Z\",\n \"stdout\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d50844f0c9f5f2f280e61\",\n \"stderr\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d50844f0c9f5f2f280e61\",\n \"exit_code\": 0\n },\n {\n \"name\": \"alignment-metrics-qc_Picard_MergeSamFiles\",\n \"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\",\n \"start_time\": \"2020-03-05T13:55:22Z\",\n \"end_time\": \"2020-03-05T14:04:15Z\",\n \"stdout\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4e5c4f0c9f5f2f27d344\",\n \"stderr\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4e5c4f0c9f5f2f27d344\",\n \"exit_code\": 0\n },\n {\n \"name\": \"alignment-metrics-qc_SBG_FlattenLists\",\n \"cmd\": \"echo \\\"Output is now a single list\\\"\",\n \"start_time\": \"2020-03-05T13:54:30Z\",\n \"end_time\": \"2020-03-05T13:54:49Z\",\n \"stdout\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\",\n \"stderr\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\",\n \"exit_code\": 0\n }\n ],\n \"outputs\": {\n \"summary_metrics\": {\n \"path\": \"drs://cgc-ga4gh-api.sbgenomics.com/5a9d50884f0c99ebf7efffdd\",\n \"size\": 2125,\n \"name\": \"HCC1143.merged.summary_metrics.txt\",\n \"class\": \"File\"\n }\n }\n}", "language": "json" } ], "sidebar": true } [/block]