Arvados

L7:"CWL workflow best practices library":https://github.com/common-workflow-language/workflows and "dockstore":http://dockstore.org

L11: Avoid s/including/declaring/ @InlineJavascriptRequirement@ (nitpicky but it follows you saying declare in L9)

L43: Similarly, you can get the designated output directory using $(runtime.outdir).

L79: Don't s/specifying/specify/ resource

L109: has to s/complete/wait/ for all samples to complete before @step2@ can start +computing+ on any samples.

L134: Instead, scatter over a subworkflow.  In this pattern, a sample can proceed -from- to @step2@ as soon as @step1@ is done, independently of any other samples. The subworkflow can also be put in a separate CWL workflow file.
Example:

otherwise LGTM. We can add new things later when we think of them.