{"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://cavatica-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: cavatica-ga4gh-api.sbgenomics.com\\nX-SBG-Auth-Token: 55e9691c111146bd384c5ec40a9f97fb1\\n\",\n      \"language\": \"http\",\n      \"name\": null\n    },\n    {\n      \"code\": \"curl --location --request POST 'https://cavatica-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs' \\\\\\n--header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \\\\\\n--header 'Cookie: language=en' \\\\\\n--form 'workflow_params={\\\"project\\\": \\\"rfranklin/my-project\\\", \\\"use_interruptible_instances\\\": true, \\\"inputs\\\": {\\\"input_bam\\\": {\\\"class\\\": \\\"File\\\", \\\"path\\\": \\\"drs://cavatica-ga4gh-api.sbgenomics.com/5f7b09a2e4b0e67085ff9386\\\"}}};type=application/json'  \\\\\\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  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n###Request body\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"When running a new workflow via WES on CAVATICA, you need to specify the target [project](doc:projects-on-cavatica) 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://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  \\\"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":"5f8943e93a9e5300121608ea","createdAt":"2020-10-16T06:55:37.695Z","user":"566590c83889610d0008a253","category":{"sync":{"isSync":false,"url":""},"pages":[],"title":"WES API","slug":"wes-api","order":29,"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","6024033e2b2f6f004dfe994c","60a7a12f9a06c70052b7c4db","60a7ab97266a4700161507c4","60b0c84babba720010a8b0b5"],"_id":"5773dcfc255e820e00e1cd50","__v":39,"createdAt":"2016-06-29T14:36:44.812Z","releaseDate":"2016-06-29T14:36:44.812Z","project":"5773dcfc255e820e00e1cd4d"},"project":"5773dcfc255e820e00e1cd4d","__v":0,"parentDoc":null}

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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://cavatica-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: cavatica-ga4gh-api.sbgenomics.com\nX-SBG-Auth-Token: 55e9691c111146bd384c5ec40a9f97fb1\n", "language": "http", "name": null }, { "code": "curl --location --request POST 'https://cavatica-ga4gh-api.sbgenomics.com/ga4gh/wes/v1/runs' \\\n--header 'X-SBG-Auth-Token: 55e9691c111146d384c5ec40a9f97fc0' \\\n--header 'Cookie: language=en' \\\n--form 'workflow_params={\"project\": \"rfranklin/my-project\", \"use_interruptible_instances\": true, \"inputs\": {\"input_bam\": {\"class\": \"File\", \"path\": \"drs://cavatica-ga4gh-api.sbgenomics.com/5f7b09a2e4b0e67085ff9386\"}}};type=application/json' \\\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": "" }, "cols": 2, "rows": 1 } [/block] ###Request body [block:callout] { "type": "info", "body": "When running a new workflow via WES on CAVATICA, you need to specify the target [project](doc:projects-on-cavatica) 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://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 \"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]