Bump CWL Version to v1.2

Bumped CWL version for all CWL workflows and steps to v1.2.

CWL v1.2 is more explicit about the way that strings in embedded code containing a dollar sign ($) must be escaped. See https://www.commonwl.org/v1.2/Workflow.html#String_interpolation. It turned out that a few workflow steps contained inline Bash code with improperly escaped variables references. This has been fixed.