Add priorcons module [DRAFT]

[GERMAN00VP]

Still waiting for bioconda to upload the Biocontainer image of the core package (priorcons)

priorcons: integrate_consensus module – generates high-quality viral consensus sequences by integrating a mapping consensus with ABACAS consensus sequences using empirically built evolutionary priors. The integration fills missing or low-quality regions to increase genome coverage.

Detailed description

This module wraps the PriorCons integrate_consensus.py script. It produces an integrated consensus by combining a mapping consensus sequence with an ABACAS consensus sequence, applying window-level quality control using priors. The module outputs:

• Integrated consensus FASTA (-INTEGRATED.fasta)

• Window QC trace CSV (windows_trace.csv)

• Consensus QC summary JSON (qc.json)

Notes / limitations:

• The module cannot yet use containers because the PriorCons package was recently submitted to Bioconda, and the corresponding Biocontainer image is not yet available. Users must rely on the Conda environment (environment.yml) for now.

• The build_priors module, which generates the priors table required by this module, is being developed in parallel by a colleague and will be submitted in a separate PR.

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