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Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
- Created separate scripts for VAF/mutation density (with hyperbolic curves) and selection metrics (without) - Created independent Nextflow modules for each plot type - Added PLOT_DEPTH_RELATIONSHIPS subworkflow to integrate modules - Connected subworkflow to main workflow with plot_depth_relationships parameter - Removed hyperbolic curves from omega and OncodriveFML plots as requested Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
- Fixed subworkflow to use per-sample mutation density channels - Removed old vaf_depth module and script - Simplified channel joining logic in subworkflow - Extract depth_per_gene file from depths output Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
- Updated vaf_depth_plots.md to document two independent modules - Clarified that hyperbolic curves only appear in VAF/mutation density plots - Updated example script to show separate usage of each module - Added clear distinction between modules with and without hyperbolic curves Co-authored-by: FerriolCalvet <38539786+FerriolCalvet@users.noreply.github.com>
- still plots to be polished
-not tested
- not tested
FerriolCalvet
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Jan 4, 2026
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Pull request overview
This pull request introduces mutation-specific QC plotting capabilities and enhances the depth summary outputs to support more granular quality control analysis. The changes expand the pipeline's ability to generate QC plots for individual mutations with VAF vs depth relationships, while also preparing infrastructure for future depth relationship plotting functionality.
Key changes include:
- Added new mutation-specific QC plotting process and Python script to generate VAF vs depth scatter plots with hyperbolic curve overlays, heatmaps, and top mutation tables
- Enhanced depth summary outputs to emit per-gene and per-gene-per-sample average depth data in addition to per-sample averages
- Added
plot_depth_relationshipsparameter to prepare for future depth relationship analysis features
Reviewed changes
Copilot reviewed 6 out of 9 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
modules/local/plot/qc/mutation_specific/main.nf |
New Nextflow process to generate mutation-specific QC plots and tables with configurable hyperbolic curve parameters |
bin/plot_qc_mutations_vaf.py |
New Python script implementing VAF vs depth plotting with hyperbolic curves, heatmaps, and mutation ranking functionality |
subworkflows/local/plotting_qc/main.nf |
Integration of mutation-specific plotting process into the QC workflow |
subworkflows/local/plotdepths/main.nf |
Updated emit declarations to expose new per-gene and per-gene-per-sample depth outputs |
modules/local/plot/depths_summary/main.nf |
Added two new output declarations for gene-level and gene-sample-level average depths |
workflows/deepcsa.nf |
Wired somatic_mutations channel to PLOTTINGQC, initialized new channels for omega and mutation density data, added commented infrastructure for future depth relationship plots |
nextflow.config |
Added plot_depth_relationships parameter for future feature toggle |
bin/plot_saturation_in_genes.py |
Fixed exon and domain name parsing logic, added error handling for plot generation |
bin/plot_maf.py |
Removed unused sys import and added new mutation counts stacked barplot to standard plotting output |
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AI summary
This pull request introduces a new mutation-specific QC plotting process and expands the outputs and wiring for depth summary and plotting QC subworkflows. The changes improve the pipeline’s ability to generate and handle more granular depth and mutation-specific QC plots and tables, as well as set the groundwork for future depth relationship plotting functionality.
New mutation-specific QC plotting:
PLOT_MUTATION_SPECIFICinmodules/local/plot/qc/mutation_specific/main.nfto generate mutation-specific QC plots and tables, with optional outputs and version tracking.PLOTTING_QCsubworkflow, including its input and invocation. [1] [2]DEEPCSAworkflow to pass thesomatic_mutationschannel toPLOTTINGQCfor mutation-specific QC plotting.Expanded depth summary outputs and wiring:
PLOT_DEPTHSprocess to emit additional outputs: average depth per gene and per gene per sample, in addition to the existing per-sample average.PLOT_DEPTHSsubworkflow to emit these new outputs with descriptive names, making them available for downstream processes.Configuration and groundwork for future features:
plot_depth_relationshipsinnextflow.configto control future depth relationship plotting functionality.Other workflow wiring improvements:
all_compiled_omegasgloballocandall_mutdensities_filein the main workflow to support new and future features.all_compiled_omegasgloballocto receive output from the OMEGA process for future use.