Document SOP

[kgostic]

Goal

We need a clear set of step-by-step instructions for running this pipeline (1) locally in the VAP and (2) in Azure Batch. This should be able to serve as an SOP for pipeline runs, and should be detailed enough that we can use it to onboard new team members to these tasks. It may also be used as a training resource if our pipeline becomes a reference implementation.

Required features

• Setup instructions
• Step by step instructions for running locally
• Step by step instructions for running in Azure Batch
• Some info about how to modify the config
• DUE for review by Weds 12/4 We will use this for the team runthrough on 12/6

[athowes]

If it's not already, I think that this SOP would ideally be a vignette.

I don't think there are barriers to doing this locally. But of course for a vignette to interact with Azure batch I can imagine there are technical challenges.

Nonetheless the benefits of this (both the local and Azure batch versions) I think are:

1. Documented in the same place as the code (the website)
2. Can be used as a type of integration test
3. If you see a vignette on the website then you can trust it is at least up to date enough to run

I think that this task or extensions of this task could be assigned to people learning about / to use the pipeline.