Resolve "samtools sort: couldn't allocate memory for bam_mem"

Fixes some newly discovered metadata errors.
Has been tested with --upload false
Testing overnight (with `--upload true --server dev

• W-RCGG: submitted stranded/spike = blank & have fastq's not matching convention
• 14-3R4R: submitted stranded/spike = unspecified
• Q-Y5HT: fastq structure error (fastq+bam concatenation)
• W-RB84: no errors

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 #105 (closed) Closes #106 (closed) Closes #107 (closed) Closes #108 (closed) Closes #109 (closed)

/cc @ghenry @venkat.malladi