If ends force then override fastq read error

Fix Endness force

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 #135 (closed)

/cc @ghenry @venkat.malladi