{"_id":"5a3a533e142db90026f24011","project":"55faf11ba62ba1170021a9a7","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":40,"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","59a555bccdbd85001bfb1442","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"55faf96917b9d00d00969f48","pages":["5626a5d644c87f0d00fe6396","5626a5e4e2ce610d004e3dd8","5626a89ce2ce610d004e3dde","56429a87f49bfa0d002f54e0"],"project":"55faf11ba62ba1170021a9a7","__v":4,"version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2015-09-17T17:33:29.016Z","from_sync":false,"order":20,"slug":"run-an-analysis","title":"RUN AN ANALYSIS"},"user":"5613e4f8fdd08f2b00437620","githubsync":"","__v":0,"parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-12-20T12:10:38.314Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"##Overview\n\nExecute apps on the CGC to perform analyses. Each app execution is called a **task**. Each task is associated with a set of input files and chosen settings for the tool(s) in the app.\n\nOn this page, learn about the different types of tasks as well as the configurable components of a task.\n\nConversely, see the step-by-step instructions for [running a task](doc:run-a-task).\n\n##About tasks\n\nA **task** is an execution of an app. Each task is associated with a set of input files and parameter settings. There are two types of tasks on the CGC:\n\n  * **Single task:** A single task represents one execution of a workflow or tool in your project. \n  * **Batch task:** Batch tasks comprise of several child tasks and are used to run the same workflow or tool multiple times with varying inputs in parallel executions. Learn more about [batch tasks](doc:about-batch-analysis).\n\nWhile you set up a task, it is in a draft state and is labelled **DRAFT**. Each **DRAFT** task is saved in the **Tasks** tab for you to set up and run whenever convenient.\n\nLearn how to [create a **DRAFT** task](doc:run-a-task#section-1-create-draft-task) as part of running an analysis.\n\n##Configure your task\n\nBelow, learn about the configurable components of your task: [inputs](doc:about-analyses#section-inputs) and [app settings](doc:about-analyses#section-app-settings).\n\n###Inputs\n\nInput files are the data on which you execute your analysis. \n\nNote that before you configure your task, input must have already been added to your project. You can [add files to a project](docs:copy-files-using-the-visual-interface) from the **Public Files Repository**, from **another project**, or by [uploading them directly to your project](doc:upload-to-the-cgc). \n\nLearn about specific types of input files below. Or, learn how to [select input files](doc:run-a-task#section-2-select-input-files) as part of running your analysis.\n\n####Reference files\n\nA reference file is a specific type of input. The CGC maintains the latest and the most frequently used reference genomes and annotation files in its **Public Reference Files** repository, so you won't have to upload your own reference files each time.\n\n####Suggested files\n\nTo help you get started with your analyses, some of the CGC public workflows in the **Public apps** gallery have suggested reference files. This feature allows you to easily add the necessary reference files to help your workflow run properly.\n\nA **Suggested files** pop-up will prompt you to add the suggested files when setting up your draft task. \n\nIf you already have all the suggested reference files in your project, they will pre-populate your draft task page. If any of your workflow's suggested files are not in your project, a **Suggested files** pop-up will prompt you to copy the missing files to your project. You can:\n\n  * Populate your task with the suggested files by clicking **Copy**.\n  * Ignore the suggested files by clicking **Don’t copy**. The pop-up is permanently dismissed and you can choose your own reference files.\n  * Postpone your decision by closing the **Suggested files** pop-up. The pop-up will appear again the next time you access this draft task. \n\n###App settings\n\nThe **Define App Settings** tab on the draft task page allows you to [set the exposed parameters](doc:run-a-task#section--3-define-app-settings) for every tool in your app. For information on exposing parameters, see the [documentation on editing an app](doc:expose-tool-parameters-for-configuration).\n\nOnly parameters marked to be exposed at runtime can be edited, but you can view all tool parameters. The View Parameters dropdown list allows you to:\n* **Show all** - Displays all editable and non-editable parameters.\n* **Show editable** - Displays editable parameters in view mode.\n* **Show non-default** - Displays parameters whose values have been modified compared to the default ones.\n\nLearn how to [define app settings](doc:run-a-task#section-3-define-app-settings) as part of running your analysis.\n\n##Resources\n* [Run a task](doc:run-a-task) \n* [About batch analyses](doc:about-batch-analyses)\n* [About task execution](doc:about-task-execution) \n* [About controlling task execution](doc:about-controlling-task-execution)","excerpt":"","slug":"about-analyses","type":"basic","title":"About analyses"}
##Overview Execute apps on the CGC to perform analyses. Each app execution is called a **task**. Each task is associated with a set of input files and chosen settings for the tool(s) in the app. On this page, learn about the different types of tasks as well as the configurable components of a task. Conversely, see the step-by-step instructions for [running a task](doc:run-a-task). ##About tasks A **task** is an execution of an app. Each task is associated with a set of input files and parameter settings. There are two types of tasks on the CGC: * **Single task:** A single task represents one execution of a workflow or tool in your project. * **Batch task:** Batch tasks comprise of several child tasks and are used to run the same workflow or tool multiple times with varying inputs in parallel executions. Learn more about [batch tasks](doc:about-batch-analysis). While you set up a task, it is in a draft state and is labelled **DRAFT**. Each **DRAFT** task is saved in the **Tasks** tab for you to set up and run whenever convenient. Learn how to [create a **DRAFT** task](doc:run-a-task#section-1-create-draft-task) as part of running an analysis. ##Configure your task Below, learn about the configurable components of your task: [inputs](doc:about-analyses#section-inputs) and [app settings](doc:about-analyses#section-app-settings). ###Inputs Input files are the data on which you execute your analysis. Note that before you configure your task, input must have already been added to your project. You can [add files to a project](docs:copy-files-using-the-visual-interface) from the **Public Files Repository**, from **another project**, or by [uploading them directly to your project](doc:upload-to-the-cgc). Learn about specific types of input files below. Or, learn how to [select input files](doc:run-a-task#section-2-select-input-files) as part of running your analysis. ####Reference files A reference file is a specific type of input. The CGC maintains the latest and the most frequently used reference genomes and annotation files in its **Public Reference Files** repository, so you won't have to upload your own reference files each time. ####Suggested files To help you get started with your analyses, some of the CGC public workflows in the **Public apps** gallery have suggested reference files. This feature allows you to easily add the necessary reference files to help your workflow run properly. A **Suggested files** pop-up will prompt you to add the suggested files when setting up your draft task. If you already have all the suggested reference files in your project, they will pre-populate your draft task page. If any of your workflow's suggested files are not in your project, a **Suggested files** pop-up will prompt you to copy the missing files to your project. You can: * Populate your task with the suggested files by clicking **Copy**. * Ignore the suggested files by clicking **Don’t copy**. The pop-up is permanently dismissed and you can choose your own reference files. * Postpone your decision by closing the **Suggested files** pop-up. The pop-up will appear again the next time you access this draft task. ###App settings The **Define App Settings** tab on the draft task page allows you to [set the exposed parameters](doc:run-a-task#section--3-define-app-settings) for every tool in your app. For information on exposing parameters, see the [documentation on editing an app](doc:expose-tool-parameters-for-configuration). Only parameters marked to be exposed at runtime can be edited, but you can view all tool parameters. The View Parameters dropdown list allows you to: * **Show all** - Displays all editable and non-editable parameters. * **Show editable** - Displays editable parameters in view mode. * **Show non-default** - Displays parameters whose values have been modified compared to the default ones. Learn how to [define app settings](doc:run-a-task#section-3-define-app-settings) as part of running your analysis. ##Resources * [Run a task](doc:run-a-task) * [About batch analyses](doc:about-batch-analyses) * [About task execution](doc:about-task-execution) * [About controlling task execution](doc:about-controlling-task-execution)