{"_id":"570bf334e516aa340041cca5","project":"55faf11ba62ba1170021a9a7","category":{"_id":"55faf95fa8a7770d00c2c0c0","__v":6,"pages":["56268b91c2781f0d00364bc2","56268ba3ad42230d00c3ea33","5637e6cffbe1c50d008cb076","56429e77f49bfa0d002f54e5","56429e85e75d700d008de10e","5642a57b5846360d000cfe26"],"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-17T17:33:19.476Z","from_sync":false,"order":17,"slug":"edit-an-app","title":"EDIT AN APP"},"parentDoc":null,"user":"5613e4f8fdd08f2b00437620","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":37,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","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"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"__v":5,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-04-11T18:55:48.555Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":4,"body":"Workflows are chains of connected tools. You can [edit any of the publicly available workflows](the-pipeline-editor) hosted on the CGC in the **Workflow Editor**. As shown below, you can also use the **Workflow Editor** to build a workflow from scratch.\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [Create a workflow](#section-create-a-workflow) \\n* [Insert tools](#section-insert-tools)\\n* [Connect tools](#section-connect-tools)\\n* [Add input and output nodes to workflows](#section-add-input-and-output-nodes-to-workflows)\\n* [Relabel tools](#section-relabel-tools)\"\n}\n[/block]\n##Create a workflow\nWorkflows are created within projects. So, to create a workflow, first [navigate to the dashboard for the project](view-a-project) that you want to work in.\n\n1. Go to the **Apps** tab, and click **+ Add app**.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/ebb65c5-create-a-wf-cgc.jpg\",\n        \"create-a-wf-cgc.jpg\",\n        1227,\n        702,\n        \"#18528d\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n 2. Click **Create New App** and then click **Create a workflow ** in the pop-up, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/b69843f-create-a-wf-cgc-2.jpg\",\n        \"create-a-wf-cgc-2.jpg\",\n        1146,\n        727,\n        \"#eaeaea\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n3. Name your workflow, and click **Create**. \n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/1d024a1-create-a-wf-cgc-3.jpg\",\n        \"create-a-wf-cgc-3.jpg\",\n        1146,\n        704,\n        \"#f8f1f8\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\nOnce you have named your new workflow, you will be taken to the Workflow Editor, shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/6867738-create-a-wf-cgc-4.jpg\",\n        \"create-a-wf-cgc-4.jpg\",\n        1167,\n        687,\n        \"#eff1f2\"\n      ],\n      \"border\": true\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Insert apps\nUse the right hand panel on the **Workflow Editor** to find apps, which will be the nodes in your workflow. You have the following options:\n\n  * **Search apps** - enter the desired keyword(s) to search for an app.\n  * **Category** - filter apps based on the category (type of analysis) they belong to (e.g. \"Variant-Calling\").\n  *   * **Toolkit** - filter apps based on their toolkit (e.g. \"SAMTools\"). Click the app name to open the app page with further information.\n\nApps are divided into:\n\n  * **My projects** are apps that you have described using the Tool Editor (for Tools) or Workflow Editor (for workflows).\n  * **Public apps** are publicly available apps on the CGC.\n\nDrag-and-drop your chosen tools onto the canvas. \n\nTools are graphically represented in the **Workflow Editor** as blue circular nodes, as shown below.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/YfRAnCI2Q2CIuFS75ehI_Screen%20Shot%202016-03-31%20at%2010.43.06%20AM.jpeg\",\n        \"Screen Shot 2016-03-31 at 10.43.06 AM.jpeg\",\n        \"440\",\n        \"444\",\n        \"#2d547c\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"If you accidentally drag-and-drop the wrong tool onto the canvas, click on the node and then click on the ‘x’ in the red circle to remove the tool from the workflow.\",\n  \"title\": \"Removing a tool from the Workflow Editor\"\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Connect tools\nThere are circles on the perimeter of each each node in the **Workflow Editor**, as shown below. These represent the tool's ports, used for data to flow in and out of. Circles on the left of the node represent input ports whereas the ones on the right indicate output ports.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/Haofr3kpSPOIsJ4Lsf58_Screen%20Shot%202016-03-31%20at%2010.43.06%20AM.jpeg\",\n        \"Screen Shot 2016-03-31 at 10.43.06 AM.jpeg\",\n        \"440\",\n        \"444\",\n        \"#2d547c\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\nClicking on a port, and dragging will reveal a smart connector. Use this to connect tools into workflows.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Add input and output nodes to workflows\nTo add an input node and connect it to a tool, drag the smart connector from the tool's input node to the far left of the the canvas. An input node will be added.\nTo add an output node to the workflow, drag the smart connector from a tool's output node to the far right of the canvas.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Relabel tools\nTo re-name a tool, click on the tool, and then select the pencil icon that appears next to the tool name.\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/fL0sOpcS4m7UGXVkaFdA_Screen%20Shot%202015-11-13%20at%2014.46.21.png\",\n        \"Screen Shot 2015-11-13 at 14.46.21.png\",\n        \"476\",\n        \"404\",\n        \"#106a47\",\n        \"\"\n      ],\n      \"caption\": \"Rename a tool\",\n      \"border\": true\n    }\n  ]\n}\n[/block]\nWhen you've finished building a workflow, click **Save** in the upper right corner.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"<a name=\"top\"></a>","slug":"create-a-workflow","type":"basic","title":"Create a workflow"}

Create a workflow

<a name="top"></a>

Workflows are chains of connected tools. You can [edit any of the publicly available workflows](the-pipeline-editor) hosted on the CGC in the **Workflow Editor**. As shown below, you can also use the **Workflow Editor** to build a workflow from scratch. [block:callout] { "type": "warning", "title": "On this page:", "body": "* [Create a workflow](#section-create-a-workflow) \n* [Insert tools](#section-insert-tools)\n* [Connect tools](#section-connect-tools)\n* [Add input and output nodes to workflows](#section-add-input-and-output-nodes-to-workflows)\n* [Relabel tools](#section-relabel-tools)" } [/block] ##Create a workflow Workflows are created within projects. So, to create a workflow, first [navigate to the dashboard for the project](view-a-project) that you want to work in. 1. Go to the **Apps** tab, and click **+ Add app**. [block:image] { "images": [ { "image": [ "https://files.readme.io/ebb65c5-create-a-wf-cgc.jpg", "create-a-wf-cgc.jpg", 1227, 702, "#18528d" ], "border": true } ] } [/block] 2. Click **Create New App** and then click **Create a workflow ** in the pop-up, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/b69843f-create-a-wf-cgc-2.jpg", "create-a-wf-cgc-2.jpg", 1146, 727, "#eaeaea" ], "border": true } ] } [/block] 3. Name your workflow, and click **Create**. [block:image] { "images": [ { "image": [ "https://files.readme.io/1d024a1-create-a-wf-cgc-3.jpg", "create-a-wf-cgc-3.jpg", 1146, 704, "#f8f1f8" ], "border": true } ] } [/block] Once you have named your new workflow, you will be taken to the Workflow Editor, shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/6867738-create-a-wf-cgc-4.jpg", "create-a-wf-cgc-4.jpg", 1167, 687, "#eff1f2" ], "border": true } ] } [/block] <div align="right"><a href="#top">top</a></div> ##Insert apps Use the right hand panel on the **Workflow Editor** to find apps, which will be the nodes in your workflow. You have the following options: * **Search apps** - enter the desired keyword(s) to search for an app. * **Category** - filter apps based on the category (type of analysis) they belong to (e.g. "Variant-Calling"). * * **Toolkit** - filter apps based on their toolkit (e.g. "SAMTools"). Click the app name to open the app page with further information. Apps are divided into: * **My projects** are apps that you have described using the Tool Editor (for Tools) or Workflow Editor (for workflows). * **Public apps** are publicly available apps on the CGC. Drag-and-drop your chosen tools onto the canvas. Tools are graphically represented in the **Workflow Editor** as blue circular nodes, as shown below. [block:image] { "images": [ { "image": [ "https://files.readme.io/YfRAnCI2Q2CIuFS75ehI_Screen%20Shot%202016-03-31%20at%2010.43.06%20AM.jpeg", "Screen Shot 2016-03-31 at 10.43.06 AM.jpeg", "440", "444", "#2d547c", "" ] } ] } [/block] [block:callout] { "type": "info", "body": "If you accidentally drag-and-drop the wrong tool onto the canvas, click on the node and then click on the ‘x’ in the red circle to remove the tool from the workflow.", "title": "Removing a tool from the Workflow Editor" } [/block] <div align="right"><a href="#top">top</a></div> ##Connect tools There are circles on the perimeter of each each node in the **Workflow Editor**, as shown below. These represent the tool's ports, used for data to flow in and out of. Circles on the left of the node represent input ports whereas the ones on the right indicate output ports. [block:image] { "images": [ { "image": [ "https://files.readme.io/Haofr3kpSPOIsJ4Lsf58_Screen%20Shot%202016-03-31%20at%2010.43.06%20AM.jpeg", "Screen Shot 2016-03-31 at 10.43.06 AM.jpeg", "440", "444", "#2d547c", "" ] } ] } [/block] Clicking on a port, and dragging will reveal a smart connector. Use this to connect tools into workflows. <div align="right"><a href="#top">top</a></div> ##Add input and output nodes to workflows To add an input node and connect it to a tool, drag the smart connector from the tool's input node to the far left of the the canvas. An input node will be added. To add an output node to the workflow, drag the smart connector from a tool's output node to the far right of the canvas. <div align="right"><a href="#top">top</a></div> ##Relabel tools To re-name a tool, click on the tool, and then select the pencil icon that appears next to the tool name. [block:image] { "images": [ { "image": [ "https://files.readme.io/fL0sOpcS4m7UGXVkaFdA_Screen%20Shot%202015-11-13%20at%2014.46.21.png", "Screen Shot 2015-11-13 at 14.46.21.png", "476", "404", "#106a47", "" ], "caption": "Rename a tool", "border": true } ] } [/block] When you've finished building a workflow, click **Save** in the upper right corner. <div align="right"><a href="#top">top</a></div>