Add missing commit from omega flagging

[FerriolCalvet]

AI summary

This pull request introduces a new QC annotation step for omega analysis and integrates it into the existing plotting QC workflow. The main changes involve adding a new process for annotating omega QC results, updating the mutation density QC process to emit the required files, and wiring these steps together in the plotting and main DeepCSA workflows.

Integration of Omega QC Annotation:

• Added a new process ANNOTATE_OMEGA_QC in modules/local/plot/qc/annotate_omega/main.nf to annotate omega QC results using annotate_omega_failing.py, with appropriate input/output handling and version tracking.
• Updated the mutation density QC process to emit compiled flagged cases as compiled_flagged for downstream use.

Workflow Integration:

• Included the new ANNOTATE_OMEGA_QC process in the PLOTTING_QC subworkflow and wired its inputs to use the omega and compiled flagged cases files. [1] [2]
• Modified the PLOTTING_QC workflow to accept all_omegas as an input, enabling the new annotation step.
• Updated the main DEEPCSA workflow to only run the plotting QC when both mutation density and omega analysis are enabled, and to pass the omega results to the plotting QC step.