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Only send kill signal when stopping jobs instead of using states

Cage, Gregory requested to merge 129-stop-job-outputs into dev

Summary of Changes

Only send kill signal when stopping jobs instead of using states. Previously was reusing stop state already in Galaxy, but this was causing issues with getting output amongst other things.

Checklist

  • The MR 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 MR does not break anything (when applicable)
  • Readme file is present and up-to-date.

Documentation Updates

Additional Notes

Closes #129 (closed)

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