Improve UMI handling and deduplication options

[edmundmiller]

Summary

Enhance UMI processing with multiple deduplication tools and improved complexity calculations.

Features to implement

• Support for seqkit and fqdedup deduplication tools
• Variable-length UMI support
• Library complexity calculations (only for UMI samples)
• Preseq integration for depth projections

Implementation details

• Create modules/local/umi_dedup with tool selection
• Add library complexity calculation module
• Integrate preseq for complexity projections
• Add UMI-aware paired-end processing

Acceptance criteria

• Multiple deduplication tool support
• Variable UMI length handling
• Library complexity metrics output
• Preseq complexity projections
• Proper paired-end UMI processing

References

• PEPPRO UMI handling approach