Add validation workflow feature #6
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RosiTea
commented
Jan 6, 2026
RosiTea
commented
- Fix GeneHitPlot: Add Rscript prefix to gene_hit_summary_plot.R invocation
- Add ValidateUnitigs workflow: New external validation module with three processes (see below)
- Add buildSigFasta: Build a FASTA file with all significant kmers/unitigs from discovery dataset
- Add and fix unitig-caller: Find significant unitigs in a new validation dataset; Update container tag to valid version 1.3.1--py311heec5c76_1; in unitigCallerSimple: Create a link between significant genes and their unitigs, skip CSV header with tail -n +2, add pyseer to Rtab conversion
- Add validation_summaries.py: Pure Python script (stdlib only, no pandas) for summarising validation results
- Update helper functions and main workflow to support validation pipeline
- Add example validation manifest and Cambridge HPC configuration
- Fix GeneHitPlot: Add Rscript prefix to gene_hit_summary_plot.R invocation - Fix buildSigFasta: Update container from python:3.11-slim to python:3.11 (requires ps command) - Fix unitig-caller: Update container tag to valid version 1.3.1--py311heec5c76_1 - Fix unitigCallerSimple: Skip CSV header with tail -n +2, add pyseer to Rtab conversion - Add ValidateUnitigs workflow: New external validation module with three processes - Add validation_summaries.py: Pure Python script (stdlib only, no pandas) for summarizing validation results - Update helper functions and main workflow to support validation pipeline - Add example validation manifest and Cambridge HPC configuration
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