All samples uploaded to One Codex are automatically classified using the One Codex Database. We also assess if your sample is a targeted loci-type (e.g. 16S, 18S, ITS), and if it appears to be, we also launch our Targeted Loci database on that sample. However there are some other workflows available to be run, depending on the sample type. You may also have your own workflows that you want to run on your samples (Click here to learn more about writing your own workflows).
In this article, we walk you through launching workflows on your samples.
The "Run Workflows" Page
Click on "Run Workflows" on the left-hand navigation bar, select your sample(s), and choose your workflow!
TIP: If you want to launch a workflow on multiple samples at the same time, instead of searching for each sample, go to your Samples page, click the option to Organize Samples as Table, select the samples you want to run the workflow on, and then from the Actions menu, choose "Run Workflows". This will take you to the Run Workflows page, with your samples pre-selected!
Finding The Workflow You Want
In the Available Workflows section, the "Options" dropdown menu can make it easier to find the workflow you are interested in. This allows you to hide or show workflows written by you, workflows written by your organization (if you are part of a One Codex Organization), workflows shared from users outside of your organization, or One Codex Workflows. Note that you might not see all of these options, depending on the various workflows you have access to.
You can also choose to show or hide draft workflows, as well as recently-run workflows.
If you need to share a workflow privately to users outside of your organization, reach out to the One Codex team through the chat box at the bottom-right of your page.
Running A Workflow
Once you find the workflow you want, and you've selected the samples you want to run it on, click "Run" on the workflow card. This will bring you to a new confirmation screen, such as the below screenshot:
In this preview, You can see the number of samples that have been selected, the workflow that you plan to run on them, and the result of confirmation (i.e. three workflows will be launched; one for each of the three samples). If you are running a workflow which has arguments, you can also set them on this screen. (Learn more about setting your arguments here).
Once you've set the arguments as needed, and confirmed your samples, click the "Run" button at the top-right of this screen. We will automatically provision servers with the required CPU/memory/storage requests, and launch the workflow!
You can view the results and details of any published workflow, right from your sample's results page. To learn more about viewing results and details of your workflows, check out this article!