flag failing omegas

[FerriolCalvet]

Missing:

• Annotate the QCs for all omega types

I ignore this because the QCs are only relevant for omega, not for omegagloballoc

[Copilot]

Pull Request Overview

This PR adds functionality to annotate omega values with QC flagging information from mutation density analysis. The changes enable the pipeline to flag gene/sample pairs that fail quality control metrics (based on z-scores) and annotate omega results accordingly.

• Adds conditional execution of PLOTTINGQC workflow based on both run_mutdensity and params.omega flags
• Introduces a new ANNOTATE_OMEGA_QC process to merge QC flagging data with omega results
• Simplifies z-score filtering logic in mutation_densities_qc.py to use absolute value comparison

Reviewed Changes

Copilot reviewed 4 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
workflows/deepcsa.nf	Added params.omega condition check and passed OMEGA.out.all_compiled to PLOTTINGQC workflow
subworkflows/local/plotting_qc/main.nf	Added ANNOTATE_OMEGA_QC process integration and new input parameter for omega data
modules/local/plot/qc/mutation_densities/main.nf	Added compiled_flagged output emission for downstream QC annotation
modules/local/plot/qc/annotate_omega/main.nf	New process to annotate omega results with QC flagging data
bin/mutation_densities_qc.py	Simplified z-score filtering logic and added compilation of all flagged cases into a single output file
bin/annotate_omega_failing.py	New script to merge QC flagging data with omega results and generate summary visualizations

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[m-huertasp]

A lot of work and things here!

I have some questions (below) on how this should work. You'll see it in the comments.
I am not sure if I am missing something but is this working as you expect?