VAPER: Add unique molecular identifiers (UMI) support

[DOH-JDJ0303]

Description of feature

Unique molecular identifiers can be used to reduce the number of PCR errors introduce during library prep and are required to reduce amplification / sequencing bias when performing intra-sample population-level analyses. VAPER should incorporate UMI QC when possible, to improve assembly quality when using PCR-based libraries. This enhancement should ideally include the following:

• Correct PCR errors using UMI
  • This normally occurs after read alignment (see UMI-Tools)
  • This should be optional and would ideally be automated (only run when UMI is detected in the FASTQ header)
• Include UMI-based adjustments in the QC summary
  • Will need to establish metrics to include