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fhdsl / FH_WDL101_Cromwell

An introduction to using Cromwell and WDL at the Fred Hutch
https://hutchdatascience.org/FH_WDL101_Cromwell/
Creative Commons Attribution 4.0 International
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add big picture section? #30

Open jayoung opened 1 year ago

jayoung commented 1 year ago

hey there,

I know I already suggested finishing up with a 'what next?' section, but here's an additional idea.

Now that I know how to run workflows, troubleshoot them etc, I still find myself a bit confused about how I would put this into practise. The material as currently presented gets deep into the weeds, which is useful/necessary. But I'm finding it hard to keep the big picture in mind.

Here's my current understanding of the big picture of how this will work in practise:

  1. (one-time only for each user) set up a cromwell database
  2. (once a week or so, when you're running workflows) fire up a cromwell server to interact with the database
  3. use the Shiny app and/or the R+fh.wdlR to run/troubleshoot/monitor workflows
  4. after a workflow runs successfully, obtain the "Workflow Output Data" table, use that to locate the output files, and likely copy them to a more permanent directory, rather than /fh/scratch

Maybe it's useful to put that in a 'recap' section, to help the reader tie together everything we've learned in the course.

Janet

vortexing commented 1 year ago

What if Chapter 3 was ACTUALLY a section about "The Care and Keeping of Cromwell" where I put the information about the FRed Hutch customizations (the current chapter 4), how you typically will interact with Cromwell at the Hutch with the bullets you have above, and some info about data management and output copying (maybe a very basic intro with the info that more details can be found in the next future class?).

THEN go into Shiny, THEN fhwdlR, then summarize but really send people directly to WDL 102?