add bbgregressions

[FerriolCalvet]

New implementation of the regressions module using the bbgregressions tool!

[Copilot]

Pull request overview

This PR replaces the existing deepCSA regressions implementation with a new bbgregressions-based subworkflow, wiring it into the main DEEPCSA workflow and updating pipeline configuration/schema accordingly.

Changes:

• Swap legacy RUNREGRESSIONS + in-repo Python regression scripts for new bbgregressions Nextflow modules (edit config → create inputs → fit models → plot).
• Update pipeline parameter schema/config to expose the new bbgr_* knobs and add a new test_regressions profile/config.
• Add default bbgregressions YAML configs for mutdensity/omega/omega globalloc regressions and update publishDir routing for the new outputs.

Reviewed changes

Copilot reviewed 15 out of 22 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Rewires the regressions block to call the new REGRESSIONS* subworkflows with bbgregressions inputs.
subworkflows/local/regressions/main.nf	Replaces legacy regressions workflow with EDITCONFIG → CREATE_INPUT → MODELS → PLOT steps.
conf/tools/regressions.config	Replaces old regressions params with new bbgr_* params and default config paths.
nextflow_schema.json	Updates schema for the new regressions parameters and UI grouping.
modules/local/bbgtools/bbgregressions/editconfig/main.nf	Adds a process to produce the final per-run bbgregressions config.
modules/local/bbgtools/bbgregressions/create_input/main.nf	Adds a process to generate regression inputs via bbgregressions.
modules/local/bbgtools/bbgregressions/regressions/main.nf	Adds a process to run bbgregressions model fitting.
modules/local/bbgtools/bbgregressions/plot/main.nf	Adds a process to plot regression results via bbgregressions.
modules/local/bbgtools/bbgregressions/*/meta.yml	Adds module metadata files (currently empty).
conf/modules.config	Adds publishDir routing for the new regressions subworkflow outputs and removes legacy RUNREGRESSIONS config.
nextflow.config	Adds a test_regressions profile including a new test config file.
conf/deepcsa_config_bbgregressions_test.config	Introduces a regressions-oriented test profile configuration.
bin/regressions_editconfig.py	New helper script to tailor bbgregressions config based on mode/metric (and omega QC results).
modules/local/runregressions/main.nf	Removes legacy regressions process.
bin/regression_analysis.py	Removes legacy regression analysis runner.
bin/utils_regressions.py	Removes legacy regression helper utilities.
assets/regressions/configs/mutdensity.yml	Adds default bbgregressions config for mutdensity.
assets/regressions/configs/omega.yml	Adds default bbgregressions config for omega.
assets/regressions/configs/omegaglobal.yml	Adds default bbgregressions config for omega global-loc.

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[FerriolCalvet]

see #442 for some comments on things that should be updated soonish