disable automatic filling of 0s in profile

[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 adds optional Bayesian smoothing for low-mutation samples when generating mutational profiles, refines omega QC flag annotation, and extends contamination QC with a SNP-site–based metric.

Changes:

• Introduce profile_smoothing parameter and wire a cohort-level prior profile into profile computation.
• Extend mut_profile.py to support smoothing via --smoothed/--prior_profile and perform the Bayesian update under a hardcoded (200) mutation threshold.
• Refactor omega-flag annotation logic and add an additional contamination QC output based on SNP sites.

Reviewed changes

Copilot reviewed 5 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
subworkflows/local/mutationprofile/main.nf	Adds cohort prior computation and passes it into per-sample profile generation when smoothing is enabled.
modules/local/compute_profile/main.nf	Extends module inputs to accept a cohort prior profile and conditionally adds CLI args for smoothing.
conf/modules.config	Plumbs params.profile_smoothing into COMPUTEPROFILE via ext.smoothing.
bin/mut_profile.py	Implements Bayesian smoothing and exposes new CLI flags to apply it.
nextflow.config	Adds params.profile_smoothing default.
nextflow_schema.json	Exposes profile_smoothing in the schema/UI.
bin/check_contamination.py	Refactors contamination entrypoints and adds SNP-based contamination proportion output.
bin/annotate_omega_failing.py	Splits flagged tables into gene/sample criteria, updates plots, and changes omega annotation merge logic.

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[koszulordie]

I focused on the mut_profile.py script and as far as I can tell everything looks correct. I commented on the definition of MUT_PROBABILITY in line 302, we can add a comment here for clarity, as this step is critical. I also suggest to provide this profile in normalized form so that the scale, although arbitrary, always displays the same range of values.

[FerriolCalvet]

we agreed this branch is ready to be merged, only pending to be fully tested with the update that removes the pseudocount of relative mutability per channel

once we merge #390