{"metadata":{"image":[],"title":"","description":""},"api":{"url":"","auth":"required","settings":"","results":{"codes":[]},"params":[]},"next":{"description":"","pages":[]},"title":"Run a workflow","type":"basic","slug":"run-a-workflow","excerpt":"","body":"This call runs (executes) a workflow and returns the run ID which you can use to monitor its progress (see [Get details of a workflow run](doc:get-details-of-a-workflow-run)). \n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs\",\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\": \"POST /ga4gh/wes/v1/runs HTTP/1.1\\nHost: cgc-ga4gh-api.sbgenomics.com\\nX-SBG-Auth-Token: 55e9691c111146bd384c5ec40a9f97fb1\\nContent-Type: multipart/form-data\\n\",\n      \"language\": \"http\",\n      \"name\": null\n    },\n    {\n      \"code\": \"curl --location --request POST 'https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs' \\\\\\n--header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \\\\\\n--header 'Cookie: language=en' \\\\\\n--header 'Content-Type: multipart/form-data' \\\\\\n--form 'workflow_params={\\\"project\\\": \\\"rfranklin/my-project\\\", \\\"use_interruptible_instances\\\": true, \\\"inputs\\\": {\\\"input_bam\\\": {\\\"class\\\": \\\"File\\\", \\\"path\\\": \\\"drs://cgc-ga4gh-api.sbgenomics.com/5f7b09a2e4b0e67085ff9386\\\"}}}' \\\\\\n--form 'workflow_type=CWL' \\\\\\n--form 'tags={}' \\\\\\n--form 'workflow_engine_parameters={}' \\\\\\n--form 'workflow_url=sbg://rfranklin/my-project/tool/0'\",\n      \"language\": \"curl\",\n      \"name\": \"cURL\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]\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    \"1-0\": \"`Content-Type`\\n_required_\",\n    \"1-1\": \"Specify: `multipart/form-data`\"\n  },\n  \"cols\": 2,\n  \"rows\": 2\n}\n[/block]\n###Request body\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"When running a new workflow via WES on CGC, you need to specify the target [project](doc:projects-on-the-platform) using the `project` parameter. See details below.\"\n}\n[/block]\n\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"Data type\",\n    \"h-2\": \"Description\",\n    \"0-0\": \"`workflow_params`\\n_required_\",\n    \"0-1\": \"object\",\n    \"0-2\": \"Specify the name of the project using the `project` (_required_) parameter , e.g. `\\\"project\\\": \\\"rfranklin/my-project\\\"`.\\n\\nYou can also use this parameter to specify the input files:\\n* The path to the files can be specified either as a platform-local DRS URI or file ID.\\n* *Option to specify files via an external DRS URI is coming soon.*\",\n    \"1-0\": \"`workflow_type`\\n_required_\",\n    \"1-1\": \"string\",\n    \"1-2\": \"The type of workflow language submitted which is [supported by this WES instance](doc:get-service-information).\",\n    \"4-0\": \"`workflow_url`\\n_required_\",\n    \"4-1\": \"string\",\n    \"4-2\": \"This parameter is used for specifying the location of the App, which can be any of the following:\\n\\n  * **App in your project** - specify the URL to the app, e.g. `sbg://admin/sbg-public-data/topmed-alignment`\\n  * **App in the Dockstore** - specify the URL to your app in the Dockstore, using the standard HTTP or TRS format\\n  * **App uploaded via `workflow_attachment` **- specify the relative path to the appropriate attachment, e.g. `#/workflow_attachment/0`\",\n    \"2-0\": \"`workflow_type_version`\\n_required_\",\n    \"2-1\": \"string\",\n    \"2-2\": \"The version of the workflow language submitted which is [supported by this WES instance](doc:get-service-information).\",\n    \"3-0\": \"`tags`\",\n    \"3-1\": \"string\",\n    \"3-2\": \"Specify tags.\",\n    \"5-0\": \"`workflow_attachment`\",\n    \"5-2\": \"The `workflow_attachment` array may be used to upload the App needed to execute the workflow.\",\n    \"5-1\": \"Array of strings <binary>\"\n  },\n  \"cols\": 3,\n  \"rows\": 6\n}\n[/block]\n##Example request body\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\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  \\\"workflow_url\\\": \\\"sbg://rfranklin/my-project/alignment-metrics-qc/0\\\"\\n}\",\n      \"language\": \"json\"\n    }\n  ]\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    \"0-1\": \"string\",\n    \"0-2\": \"Workflow run ID\"\n  },\n  \"cols\": 3,\n  \"rows\": 1\n}\n[/block]\n###Example response body\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"{\\n  \\\"run_id\\\": \\\"103e7bc8-224e-4c97-9664-6f98a2cb7e2d\\\"\\n}\",\n      \"language\": \"json\"\n    }\n  ],\n  \"sidebar\": true\n}\n[/block]","updates":[],"order":1,"isReference":false,"hidden":false,"sync_unique":"","link_url":"","link_external":false,"_id":"5f894d5ca0ab340025c77f38","createdAt":"2020-10-16T07:35:56.003Z","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

Run a workflow

This call runs (executes) a workflow and returns the run ID which you can use to monitor its progress (see [Get details of a workflow run](doc:get-details-of-a-workflow-run)). [block:code] { "codes": [ { "code": "https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs", "language": "text", "name": "Path" } ] } [/block] ##Request ###Example request [block:code] { "codes": [ { "code": "POST /ga4gh/wes/v1/runs HTTP/1.1\nHost: cgc-ga4gh-api.sbgenomics.com\nX-SBG-Auth-Token: 55e9691c111146bd384c5ec40a9f97fb1\nContent-Type: multipart/form-data\n", "language": "http", "name": null }, { "code": "curl --location --request POST 'https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs' \\\n--header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \\\n--header 'Cookie: language=en' \\\n--header 'Content-Type: multipart/form-data' \\\n--form 'workflow_params={\"project\": \"rfranklin/my-project\", \"use_interruptible_instances\": true, \"inputs\": {\"input_bam\": {\"class\": \"File\", \"path\": \"drs://cgc-ga4gh-api.sbgenomics.com/5f7b09a2e4b0e67085ff9386\"}}}' \\\n--form 'workflow_type=CWL' \\\n--form 'tags={}' \\\n--form 'workflow_engine_parameters={}' \\\n--form 'workflow_url=sbg://rfranklin/my-project/tool/0'", "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": "", "1-0": "`Content-Type`\n_required_", "1-1": "Specify: `multipart/form-data`" }, "cols": 2, "rows": 2 } [/block] ###Request body [block:callout] { "type": "info", "body": "When running a new workflow via WES on CGC, you need to specify the target [project](doc:projects-on-the-platform) using the `project` parameter. See details below." } [/block] [block:parameters] { "data": { "h-0": "Name", "h-1": "Data type", "h-2": "Description", "0-0": "`workflow_params`\n_required_", "0-1": "object", "0-2": "Specify the name of the project using the `project` (_required_) parameter , e.g. `\"project\": \"rfranklin/my-project\"`.\n\nYou can also use this parameter to specify the input files:\n* The path to the files can be specified either as a platform-local DRS URI or file ID.\n* *Option to specify files via an external DRS URI is coming soon.*", "1-0": "`workflow_type`\n_required_", "1-1": "string", "1-2": "The type of workflow language submitted which is [supported by this WES instance](doc:get-service-information).", "4-0": "`workflow_url`\n_required_", "4-1": "string", "4-2": "This parameter is used for specifying the location of the App, which can be any of the following:\n\n * **App in your project** - specify the URL to the app, e.g. `sbg://admin/sbg-public-data/topmed-alignment`\n * **App in the Dockstore** - specify the URL to your app in the Dockstore, using the standard HTTP or TRS format\n * **App uploaded via `workflow_attachment` **- specify the relative path to the appropriate attachment, e.g. `#/workflow_attachment/0`", "2-0": "`workflow_type_version`\n_required_", "2-1": "string", "2-2": "The version of the workflow language submitted which is [supported by this WES instance](doc:get-service-information).", "3-0": "`tags`", "3-1": "string", "3-2": "Specify tags.", "5-0": "`workflow_attachment`", "5-2": "The `workflow_attachment` array may be used to upload the App needed to execute the workflow.", "5-1": "Array of strings <binary>" }, "cols": 3, "rows": 6 } [/block] ##Example request body [block:code] { "codes": [ { "code": "{\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 \"workflow_url\": \"sbg://rfranklin/my-project/alignment-metrics-qc/0\"\n}", "language": "json" } ] } [/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`", "0-1": "string", "0-2": "Workflow run ID" }, "cols": 3, "rows": 1 } [/block] ###Example response body [block:code] { "codes": [ { "code": "{\n \"run_id\": \"103e7bc8-224e-4c97-9664-6f98a2cb7e2d\"\n}", "language": "json" } ], "sidebar": true } [/block]