Prior cons buildpriors [DRAFT]

[zhliUU]

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 build-priors.py script https://github.com/GERMAN00VP/PriorCons/blob/c5e40c86fe88e617637e897cc92bd2540bc60649/priorcons/build_priors.py, it takes a fastq-aln file, name of the fastq header, and output a .parquet file.

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.

PR checklist

• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • [ ] nf-core modules test priorcons/build_priors --profile docker
    • [ ] nf-core modules test priorcons/build_priors --profile singularity
    • [x] nf-core modules test priorcons/build_priors --profile conda

[mashehu]

please use seqera containers to make it usable for docker and singularity https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers

[mashehu]

nevermind, @GERMAN00VP was faster 🙂