Prior cons buildpriors [DRAFT] #9300
Open
+228
−0
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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