Add support for CODEC sequencing data

[nh13]

Description of feature

Is your feature request related to a problem?

The fastquorum pipeline currently supports duplex sequencing (via CallDuplexConsensusReads) and simplex/standard UMI sequencing (via CallMolecularConsensusReads). However, it does not support CODEC (Concatenating Original Duplex for Error Correction) sequencing, a method that provides 1,000-fold higher accuracy than standard NGS by physically linking Watson and Crick strands (https://pubmed.ncbi.nlm.nih.gov/37106072/).

fgbio v3.0+ includes CallCodecConsensusReads specifically for CODEC data, but fastquorum does not yet utilize this tool.

Describe the solution you'd like

Add CODEC sequencing support to fastquorum, including:

1. New consensus calling pathway: Add conditional logic to invoke fgbio CallCodecConsensusReads when --protocol codec (or similar parameter) is
   specified
2. Read structure support: Document the expected CODEC read structure (typically 3M2S+T 3M2S+T - 3bp UMI, 2bp skip, template for both reads)
3. GroupReadsByUmi configuration: CODEC requires --strategy adjacency or --strategy identity (NOT paired) per the
   http://fulcrumgenomics.github.io/fgbio/tools/latest/CallCodecConsensusReads.html
4. CODEC-specific metrics: Consider adding appropriate QC metrics for CODEC consensus generation
5. Test data: Add CODEC test data to nf-core/test-datasets (may need to be synthetic/simulated given data availability constraints)

Implementation notes

• fgbio tool: http://fulcrumgenomics.github.io/fgbio/tools/latest/CallCodecConsensusReads.html
• Key parameters: --input, --output, --min-input-base-quality, --min-read-pairs, --rejects, --stats
• Reference pipeline: https://github.com/broadinstitute/CODECsuite (Broad Institute)

Additional context

CODEC sequencing is gaining adoption for high-accuracy applications including:

• Rare mutation detection
• Liquid biopsy analysis
• Microsatellite instability (MSI) detection
• Clonal hematopoiesis analysis

Related resources:

• https://github.com/fulcrumgenomics/fgbio/releases/tag/3.0.0
• https://www.nature.com/articles/s41588-023-01376-0
• https://github.com/broadinstitute/CODECsuite
• https://github.com/broadinstitute/Methyl-CODEC

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Sources:

• https://www.nature.com/articles/s41588-023-01376-0
• https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs003255.v1.p1
• https://github.com/broadinstitute/CODECsuite
• http://fulcrumgenomics.github.io/fgbio/tools/latest/
• https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
• https://nf-co.re/fastquorum/dev/