Workflow invocation improvements

[andrewfayres]

Summary of Changes

Main changes here:

• added option when getting workflow jobs of whether or not filter only running jobs. Previously, we always filtered down to running jobs.
• improved the wait_for_results method. Due to some quirks with galaxy, the call to galaxy would sometimes hang if the workflow had an error. The result is this wouldn't return until the default timeout which was quite long (30 minutes or so). Changed it so that we periodically check if it's in a terminal state. If not we check the state of the jobs to look for an error. If we find one we return.

Checklist

• The PR has a clear and concise title
• Code is self-documented and follows style guidelines.
• Automated tests are written and pass successfully.
• Regression tests (e.g. manually triggered system tests, manual GUI/tool tests, ...) are performed to make sure the PR does not break anything (when applicable)
• Readme file is present and up-to-date.

[gecage952]

Seems reasonable to me overall pending above comment.