Resolve "Change Single Read to Single End for submitted endness"

Cumulative branch for v2.0.0

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• [ ] Documentation in docs is updated
• Replace dag.png with the most recent CI pipeline integrated_pe artifact
• [ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact
• [ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact
• CHANGELOG.md is updated
• [ ] README.md is updated
• [ ] LICENSE.md is updated with new contributors
• [ ] Docker images moved to production release and changed in pipeline
• [ ] Docker images used in the CI unit tests match those used in pipeline

• Close issue
  Closes #110 (closed) Closes #114 (closed) Closes #115 (closed) Closes #70 (closed) Closes #111 (closed) Closes #112 (closed) Closes #100 (closed) Closes #95 (closed)

/cc @ghenry @venkat.malladi