chapter 4 confusion

[jayoung]

hey,

chapter 4 (Fred Hutch customizations) is confusing to me right now, for some inter-related reasons:

1. a lot of this stuff doesn't make a lot of sense to me YET because I know nothing about the WDL language. Not sure how best to handle that - maybe a chapter 3.5 that covers the very basics of WDL? or simply direct the learner to an external WDL basics tutorial? Also maybe more obviously point me to examples within the diy-cromwell-server/testWorkflows files where we actually use these parameters. I do find them when I go digging for them.

2. there's a statement in section 4.2: "you can edit these in the config file if you’d like OR you can specify these variables in your runtime block in each task to change only the variables you want to change from the default for that particular task.". Presumably that applies to the standard variables AND the Hutch custom variables? Might make sense to split out discussion of the variables themselves from HOW we can specify those variables.

3. what is the config file mentioned in 4.2? is it the cromUserConfig.txt file we used when we spun up our cromwell server? or something that's specific to an individual workflow? I think I can see examples in diy-cromwell-server/testWorkflows where you customize within the runtime blocks, but I'm not sure whether there's an example using a config file.

4. Section 4.4: perhaps split that to a separate chapter? it's not about customizing the workflows. This would be a good location for the links to external WDL docs that I was already suggesting you move from their current location

5. "We'll discuss some of the available customizations to help you run WDLs on our cluster in a simple way that still allows those workflows to be portable to other computing platforms." If I understand this right, I can have something like partition: "campus-new" in a WDL and it would still run on a non-Hutch system? Or do you mean I could run it using the fh-S3-AWS configuration just as easily as I can on the in-house cluster, but maybe that campus-new setting would make things crash on a totally external system?

In terms of my own learning, I think I kind of understand how to customize, but I think this doc could be laid out more clearly.

thanks!

j