{"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 started

Cavatica Projects

Find apps

Bring your private data

Set metadata associated with a file

Collaborate securely

BRING YOUR TOOLS

Docker

Developer tools

EDIT AN APP

Tool wrapping tips and tricks

Describe your tool (Legacy)

Browse public datasets

Run an analysis

Task Execution

Review a task

Kids First studies

Cavatica Datasets

Cavatica API

Connect cloud storage

SBFS (Beta)

BULK API ACTIONS

ASYNC BULK ACTIONS

DRS API

WES API

CAVATICA DATASETS API (Advanced Access)

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://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]