Add minor fixes

[FerriolCalvet]

No description provided.

[Copilot]

Pull request overview

This PR applies several small plotting/output-path adjustments across Nextflow modules and helper scripts, plus adds an R utility script for cord-blood mutation-rate analysis.

Changes:

• Update plotting modules/scripts to write figures into new subfolders (e.g., side_figures/, domains/) and adjust Nextflow mkdir accordingly.
• Adjust PLOT_SATURATION outputs to split PNGs vs PDFs and update ANALYZEDEPTHSGROUPS publish directory path.
• Add an R script to compute/plot corrected trinucleotide mutation rates; add a new contamination QC plot and refactor coverage plotting logic.

Reviewed changes

Copilot reviewed 3 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
modules/local/plot/selection_metrics/main.nf	Creates side_figures/ directory for side-plot outputs.
modules/local/plot/saturation/main.nf	Changes declared plot outputs and creates domains/ subdir for saturation plots.
conf/modules.config	Updates ANALYZEDEPTHSGROUPS publishDir output path.
bin/plot_selectionsideplots.py	Writes side figures into outdir/side_figures.
bin/plot_gene_saturation.py	Writes cohort-level domain-selection PNGs into a domains/ subfolder.
bin/panels_computedna2protein.py	Refactors coverage summarization to attempt DNA/Protein/Exon-level plots.
bin/cordblood_mutrate_genome_trint_corrected.R	New script to compute corrected mutation rates + plots.
bin/check_contamination.py	Adds a violin+swarm PDF summarizing somatic SNP proportions across samples.

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