The following walkthrough will take users through the steps to running a workflow on Cavatica. The instruction begins from the perspective of a user that has logged in for the first time. Users will be asked to create a project, copy a public app workflow, construct a task, and run that task.
The first step is to create a project. To do this, click the Projects drop-down menu then click + Create A Project. Next, a popup will appear and ask for more information about the project. Give the project a name then review the other options. For the example below, a personal Billing Group is selected, Location is set to AWS (us-east-1) as CHOP is located on the East Coast, Spot Instances are on, and Memoization is off. These last two options can be changed on a task by task basis.
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Once the project is created, a number of other steps can be taken to make the project more accessible. Adding a description and inviting new members are important steps to contextualize the work and disseminate results.
The next step is to obtain the KFDRC Alignment Public App. To obtain the app, click the Public Apps tab. This tab takes the user to a new page where they can search or browse the public apps available. To find the KFDRC Alignment Public App, enter KFDRC into the text box and press return. Cavatica will return all the public apps that match that description, including the alignment public app of interest. In the box of the desired app, click the Copy button. A popup will appear that asks the user to specify which project they wish to copy to. Click the Select a project drop-down menu and click the name of the project created in Step 1. Confirm the selection by again clicking the Copy button. A small popup will appear to inform the user that An app has been copied to their project. Clicking the link in that popup will take the user directly to the Apps page of their project.
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The next step is to start building a task. If not already on the Apps tab, click the tab in the top left of the project page. Next, find the alignment app and click run. While not an absolute, most KFDRC public apps come with suggested files for the input reference files. These suggested files are the often the same files used in production at KFDRC. These files are free to use at the user's discretion. For this example, click Copy to pull in the suggested files.
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Pulling in the suggested files populates most but not all of the input fields. As users can see some fields are still required but empty. Cavatica prompts users to include the missing fields with red boxes and warning messages.
One of the remaining fields asks users to provide an input bam. There are multiple ways to provide such a file. One way is to add a public test file from Cavatica. To add a public file, first open the Files page in a new tab. Next, click the + Add a File link. This link takes you to a new page with all the publically available test files from Cavatica. Users can filter this list on a number of criteria like file type. Click the drop-down menu for Type and select BAM. Some of the BAMs have associated colored tags that describe features of the file. Since the alignment app is for realigning WGS DNA samples check the box next to the file with the tag WGS. Next click the Copy to Project box. Clicking this box will cause a popup to appear. The popup will ask users if they wish to add or remove any tags to the file before copying it to the user's project. Once the user is happy with the tags, they can click the Copy box to begin the copy. The user will then be returned to their Files tab and informed of the ongoing process.
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While these test files are nice for testing a workflow, more often than not the user will have files they wish to process. In this case, they will need to upload those files to Cavatica. There are numerous ways to upload a file to Cavatica. Users are encouraged to explore these options on their own. Some of the more common methods of upload: