{"_id":"5a3a52e49fb104001ecd585e","project":"5773dcfc255e820e00e1cd4d","version":{"_id":"5773dcfc255e820e00e1cd50","__v":27,"project":"5773dcfc255e820e00e1cd4d","createdAt":"2016-06-29T14:36:44.812Z","releaseDate":"2016-06-29T14:36:44.812Z","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"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"5a3a52b5bcc254001c4bf152","project":"5773dcfc255e820e00e1cd4d","version":"5773dcfc255e820e00e1cd50","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2017-12-20T12:08:21.441Z","from_sync":false,"order":8,"slug":"run-an-analysis","title":"Run an analysis"},"user":"5613e4f8fdd08f2b00437620","githubsync":"","__v":0,"parentDoc":null,"metadata":{"title":"","description":"","image":[]},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-12-20T12:09:08.374Z","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 Cavatica 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 Cavatica:\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](https://docs.sevenbridges.com/v1.0/docs/upload-to-the-seven-bridges-platform). \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. Cavatica 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 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 **App Settings** section under the **Task Inputs** 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)","excerpt":"","slug":"about-analyses","type":"basic","title":"About analyses"}
##Overview Execute apps on Cavatica 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 Cavatica: * **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](https://docs.sevenbridges.com/v1.0/docs/upload-to-the-seven-bridges-platform). 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. Cavatica 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 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 **App Settings** section under the **Task Inputs** 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)