Some suggestions

[nsheff]

Here are a few things I found confusing as I went through the user guide:

• On this page: https://www.commonwl.org/user_guide/07-containers/index.html it's confusing that the hello.js file is made on the command line, while other files are copy+paste. I think this shows up on other pages as well. I was wondering where the hello.js file came from since all the other files I made manually. I think it would be easier for the user to follow if this was consistent.

• the same page says "baseCommand: node tells CWL that we will be running this command in a container". This confused me. Is "node" some kind of special command? Does that mean you can't have a native command named 'node' ? How exactly does that tell CWL that we will be running this in a container? Why doesn't CWL us the DockerRequirement hint/requirement to tell if it's running in a container, and how would you run a different command in a container?

• The example tool here: (https://www.commonwl.org/user_guide/17-metadata/index.html) is running wc -l on a binary file (bam format), which doesn't make sense. maybe this is just a non-working example, but still, it would be nice if the examples made sense