{"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://cavatica-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: cavatica-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://cavatica-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://cavatica-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://cavatica-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://cavatica-ga4gh-api.sbgenomics.com/5a9d50844f0c9f5f2f280e61\\\",\\n      \\\"stderr\\\": \\\"drs://cavatica-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://cavatica-ga4gh-api.sbgenomics.com/5a9d4e5c4f0c9f5f2f27d344\\\",\\n      \\\"stderr\\\": \\\"drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/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://cavatica-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\\\",\\n      \\\"stderr\\\": \\\"drs://cavatica-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\\\",\\n      \\\"exit_code\\\": 0\\n    }\\n  ],\\n  \\\"outputs\\\": {\\n    \\\"summary_metrics\\\": {\\n      \\\"path\\\": \\\"drs://cavatica-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":"5f894511e0a9c6005907c9e3","createdAt":"2020-10-16T07:00:33.867Z","user":"566590c83889610d0008a253","category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"WES API","slug":"wes-api","order":25,"from_sync":false,"reference":false,"_id":"5f893e508c9862002d0614a9","createdAt":"2020-10-16T06:31:44.321Z","version":"5773dcfc255e820e00e1cd50","project":"5773dcfc255e820e00e1cd4d","__v":0},"version":{"version":"1.0","version_clean":"1.0.0","codename":"","is_stable":true,"is_beta":false,"is_hidden":false,"is_deprecated":false,"categories":["5773dcfc255e820e00e1cd51","5773df36904b0c0e00ef05ff","577baf92451b1e0e006075ac","577bb183b7ee4a0e007c4e8d","577ce77a1cf3cb0e0048e5ea","577d11865fd4de0e00cc3dab","578e62792c3c790e00937597","578f4fd98335ca0e006d5c84","578f5e5c3d04570e00976ebb","57bc35f7531e000e0075d118","57f801b3760f3a1700219ebb","5804d55d1642890f00803623","581c8d55c0dc651900aa9350","589dcf8ba8c63b3b00c3704f","594cebadd8a2f7001b0b53b2","59a562f46a5d8c00238e309a","5a2aa096e25025003c582b58","5a2e79566c771d003ca0acd4","5a3a5166142db90026f24007","5a3a52b5bcc254001c4bf152","5a3a574a2be213002675c6d2","5a3a66bb2be213002675cb73","5a3a6e4854faf60030b63159","5c8a68278e883901341de571","5cb9971e57bf020024523c7b","5cbf1683e2a36d01d5012ecd","5dc15666a4f788004c5fd7d7","5eaff69e844d67003642a020","5eb00899b36ba5002d35b0c1","5eb0172be179b70073dc936e","5eb01b42b36ba5002d35ebba","5eb01f202654a20136813093","5eb918ef149186021c9a76c8","5f0839d3f4b24e005ebbbc29","5f893e508c9862002d0614a9"],"_id":"5773dcfc255e820e00e1cd50","__v":35,"createdAt":"2016-06-29T14:36:44.812Z","releaseDate":"2016-06-29T14:36:44.812Z","project":"5773dcfc255e820e00e1cd4d"},"project":"5773dcfc255e820e00e1cd4d","__v":0,"parentDoc":null}

Get details of a workflow run


This call returns detailed information about the specified workflow run. [block:code] { "codes": [ { "code": "https://cavatica-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: cavatica-ga4gh-api.sbgenomics.com\nX-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0\n", "language": "http", "name": null }, { "code": "curl --location --request GET 'https://cavatica-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://cavatica-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://cavatica-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://cavatica-ga4gh-api.sbgenomics.com/5a9d50844f0c9f5f2f280e61\",\n \"stderr\": \"drs://cavatica-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://cavatica-ga4gh-api.sbgenomics.com/5a9d4e5c4f0c9f5f2f27d344\",\n \"stderr\": \"drs://ga4gh-api.sb.biodatacatalyst.nhlbi.nih.gov/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://cavatica-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\",\n \"stderr\": \"drs://cavatica-ga4gh-api.sbgenomics.com/5a9d4c214f0c99ebf7eff9bf\",\n \"exit_code\": 0\n }\n ],\n \"outputs\": {\n \"summary_metrics\": {\n \"path\": \"drs://cavatica-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]