Add profile smoothing and contamination check

[FerriolCalvet]

• Add the option to smooth the mutational profile when having less than 200 mutations in the sample (this is hardcoded since we conducted entropy tests to define the threshold).
• Fix the flagging of omegas.
• Added the computation of proportion of SNP sites mutated to inform contamination in samples independent from the samples being analyzed in the same batch/cohort.

[Copilot]

Pull request overview

This PR introduces optional Bayesian smoothing for mutational profiles (using a cohort-derived prior profile), adjusts omega-flagging/visualization logic, and adds an additional contamination indicator based on the proportion of mutated SNP sites.

Changes:

• Add a profile_smoothing parameter and plumb a cohort prior profile into COMPUTE_PROFILE to enable smoothing for low-mutation samples.
• Extend mut_profile.py with Bayesian update logic and new CLI flags (--smoothed, --prior_profile).
• Refactor contamination checking to include SNP-site mutation proportion output and revise omega-flagging annotation/plots.

Reviewed changes

Copilot reviewed 5 out of 8 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
subworkflows/local/mutationprofile/main.nf	Adds cohort prior computation and passes it into profile computation when smoothing is enabled.
nextflow_schema.json	Adds profile_smoothing parameter to the schema.
nextflow.config	Adds default params.profile_smoothing = false.
modules/local/compute_profile/main.nf	Extends module inputs and wires new smoothing args into the mut_profile.py profile call.
conf/modules.config	Adds config hook intended to toggle smoothing based on params.profile_smoothing.
bin/mut_profile.py	Implements Bayesian smoothing and exposes CLI options to activate it.
bin/check_contamination.py	Refactors loading and adds SNP-based contamination summary output.
bin/annotate_omega_failing.py	Splits flagged tables by criteria and updates annotation/plotting functions accordingly.

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