Prior cons buildpriors [DRAFT] #9300
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This module builds empirical priors from alignment data for the priorcons tool. Key features: - Takes alignment file (.aln) and reference sequence ID as inputs - Outputs priors in Parquet format - Supports configurable window size and overlap via task.ext.args - Follows nf-core conventions: only input/output files as CLI params 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Add nf-test configuration with RSV test data from GitHub - Generate test snapshots with MD5 validation for output verification - Fix command syntax from buildpriors to build-priors - Remove unnecessary nextflow.config from tests folder - Tests validate both regular execution and stub mode 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Rename tests from "rsv - fasta alignment" to "build_priors_testfiles" - Update snapshots with new test names - Remove obsolete snapshot entries 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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please use seqera containers to make it usable for docker and singularity https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers |
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nevermind, @GERMAN00VP was faster 🙂 |
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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:
PR checklist
nf-core modules test priorcons/build_priors --profile dockernf-core modules test priorcons/build_priors --profile singularitynf-core modules test priorcons/build_priors --profile conda