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CWL Run Enhancements #364

@jmchilton

Description

@jmchilton
  • Suppress extra output when running --conformance-test. (Fixed with More complete I/O capturing. #368)
  • "Stage" files out of Galaxy.
  • Implement additional options available to reference tool.
    • Conditional Docker support.
  • Allow running the reference implementation this way.

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