Update mutation rate to mutation density

[FerriolCalvet]

• Update naming everywhere
• Remove per KB normalization in the file to avoid redundant information that is not being used.
• Compute mutation density for SNVs (alone), Indels (alone), SNVs + Indels (alone) and then all mutations together.

Decide if we want to update the term for mutated reads rate, and call it mutation burden or whatever we prefer? POSTPONED

• Define other_sample_SNP based on all VAFs values

AI generated summary

This pull request introduces a major refactor across multiple configuration and module files to replace the term "mutation rate" with "mutation density." The changes are primarily aimed at improving clarity and consistency in terminology throughout the codebase. Additionally, several files and processes have been renamed to align with this updated terminology.

Terminology Update: Mutation Rate to Mutation Density

• Configuration Files: Updated parameter names from mutationrate to mutationdensity across multiple configuration files, including conf/bladder.config, conf/kidney.config, conf/lung.config, and others. This ensures consistency in terminology. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
• Regression Configurations: Renamed mutrate_regressions to mutdensity_regressions in regression-related configuration files to reflect the updated terminology. [1] [2]

File and Process Renaming

• Tool Configurations: Renamed conf/tools/mutrate.config to conf/tools/mutdensity.config and updated process names within the file, such as SUBSETMUTRATE to SUBSETMUTDENSITY. [1] [2] [3] [4] [5]
• Main Modules: Renamed modules/local/computemutrate/main.nf to modules/local/computemutdensity/main.nf and updated process names and scripts accordingly, including switching from compute_mutrate.py to compute_mutdensity.py. [1] [2] [3]

Script and Argument Adjustments

• Module Processes: Updated arguments and folder names in scripts to reflect the new terminology, such as changing expected_mutrate to expected_mutdensity in the EXPECTED_MUTATED_CELLS process.
• Omega Preprocessing: Modified the synonymous mutation rates file reference from mutrates_per_gene.tsv to mutdensities_per_gene.tsv in the OMEGA_PREPROCESS process.

Removal of Redundant Code

• Oncodrive3D Module: Removed unused args variable in the ONCODRIVE3D_PLOT_CHIMERAX process, simplifying the script.

These changes collectively improve the clarity of the codebase by unifying terminology and aligning file and process names with the updated concept of "mutation density."

[Copilot]

Pull Request Overview

This PR replaces the term “mutation rate” with “mutation density” across scripts and configurations, removes per-KB normalization, and updates the compute step to use a dedicated compute_mutdensity.py for SNVs, indels, combined SNV+indel, and all-mutation densities.

• Renamed output directories, script names, process labels, and file suffixes from mutrate/mutrates to mutdensity/mutdensities
• Updated configuration parameters (mutationrate → mutationdensity, mutrate_regressions → mutdensity_regressions) and included the new mutdensity.config
• Changed the compute process from MUTRATE to MUTATION_DENSITY, switching from compute_mutrate.py to compute_mutdensity.py

Reviewed Changes

Copilot reviewed 35 out of 35 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
modules/local/mutated_cells_expected/main.nf	Renamed output dir and script argument to expected_mutdensity
modules/local/computemutdensity/main.nf	Renamed process, outputs, script call, and output file suffix to density
modules/local/indels/main.nf	Updated output filename for indels comparisons
conf/tools/regressions.config	Renamed regression parameter to mutdensity_regressions
conf/modules.config	Swapped in mutdensity.config for the old mutrate.config
(multiple conf/*.config)	Changed mutationrate flags to mutationdensity

Comments suppressed due to low confidence (4)

modules/local/bbgtools/oncodrive3d/plot_chimerax/main.nf:20

• [nitpick] The args variable was removed; if users previously passed custom arguments via task.ext.args, consider documenting this change or restoring support for extensibility.

    script:

modules/local/mutated_cells_expected/main.nf:28

• The directory is renamed from expected_mutrate to expected_mutdensity; ensure mutgenomes_expected_mutrisk.R has been updated to output into this new directory name.

    mkdir expected_mutdensity

modules/local/computemutdensity/main.nf:16

• Changing prefix to sample_name alters the output filename pattern; verify downstream processes expect ${sample_name}.${panel_version}.mutdensities.tsv and update any file‐matching logic accordingly.

    def sample_name = "${meta.id}"

conf/tools/regressions.config:8

• After renaming mutrate_regressions to mutdensity_regressions, verify all pipeline components that previously referenced the old parameter are updated to use the new one to avoid runtime errors.

    mutdensity_regressions                = null

[FerriolCalvet]

functional testing works

I have not tested the results, but they should be the same

[FedericaBrando]

Very good Ferriol! 🚀

Given our talk here I summarize the comments:

• Add a docstring at the beginning of the file explaining in very few sentences the definition of mutation density (gene and sample)
• Modularize the compute_mutdensity() to 3 parts:
  • preprocessing where you read and load dfs, subsets depths etc
  • call mutdensity_sample() (once)
  • call mutdensity_gene() (once)
• Make variable with mutation types (SNV, INSERTION, DELETION) etc at top of the script to be shared between mutdensity functions (DRY principle)
• Avoid calling the mutdensity functions several times, include the concats in the function itself.

This would improve readability and modularity of the script! Almost there 😎

[FerriolCalvet]

• Check that the outputs are the same after this code upgrade

[FedericaBrando]

Way cleaner this way! Thanks for the effort! 💯

I added a small comment and then, after testing that nothing change, it can be merged into dev!