Add mutdensity subgenic and fix bugs

[FerriolCalvet]

This PR includes the restructurization of the calls to EXPANDREGIONS to obtain a value of mutation density for subgenic regions defined from exons or domains.
It also includes some bug fixing for cases where the DNA2PROTEINMAPPING fails and then omega was not executed leading to other errors downstream.

AI summary

This pull request introduces a new workflow for enriching genomic panels with subgenic regions and refactors how panels are expanded and used throughout the pipeline. It also upgrades the omega tool version and improves reproducibility and flexibility in several processes. The changes streamline the workflow, making panel enrichment modular and easier to maintain, and ensure that downstream analyses use the correct, enriched panels.

Workflow and Pipeline Refactoring

• Added a new ENRICHPANELS workflow (subworkflows/local/enrichpanels/main.nf) to handle the enrichment of consensus panels with subgenic regions, domains, and exons. This workflow centralizes and modularizes region expansion logic.
• Refactored the main workflow (workflows/deepcsa.nf) to use the new ENRICHPANELS workflow for generating expanded panels and subgenic region JSONs, and updated downstream processes (e.g., mutation density, OMEGA analysis) to use these enriched panels instead of the original ones. [1] [2] [3] [4]
• Removed the direct use of the EXPAND_REGIONS process from the OMEGA analysis subworkflow, delegating all panel expansion to the new enrichment workflow. [1] [2] [3]

Process and Container Updates

• Updated all OMEGA-related processes (OMEGA_PREPROCESS, OMEGA_MUTABILITIES, OMEGA_ESTIMATOR) to use the new docker.io/bbglab/omega:0.2.1 container instead of the previous one, and improved version reporting by dynamically capturing the actual tool version at runtime. [1] [2] [3] [4] [5] [6] [7] [8]

Panel Expansion and Subgenic Regions

• Replaced all references to "hotspots" with "subgenic" regions in the EXPAND_REGIONS process, including output file names and script logic, to better reflect the expanded panel content. [1] [2]
• Improved logic for handling optional inclusion of exons, domains, and custom subgenic regions, making the workflow more flexible and robust to different parameter settings. [1] [2]

Error Handling and Configuration

• Added a custom error strategy for the DNA2PROTEINMAPPING process, allowing up to two retries before ignoring errors, which increases pipeline robustness.

Miscellaneous Improvements

• Simplified and clarified output handling in various subworkflows, ensuring that only the first file from multi-file outputs is used where appropriate.
• Cleaned up and removed unused or outdated code and comments for better maintainability. [1] [2]

These changes collectively improve the modularity, maintainability, and reliability of the pipeline, especially around the management and enrichment of gene panels.

[Copilot]

Pull request overview

This pull request introduces a modular workflow for enriching genomic panels with subgenic regions (exons/domains) and refactors the mutation density calculation and OMEGA analysis pipelines to use these enriched panels. The changes also upgrade the OMEGA tool to version 0.2.1, improve error handling for DNA to protein mapping failures, and standardize terminology from "hotspots" to "subgenic regions" throughout the codebase.

• Adds a new ENRICHPANELS workflow to centralize panel expansion logic with subgenic regions
• Updates all mutation density and OMEGA processes to use enriched panels instead of original consensus panels
• Upgrades OMEGA container image and improves version reporting for better reproducibility

Reviewed changes

Copilot reviewed 9 out of 13 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Integrates the new ENRICHPANELS workflow and updates downstream processes (mutation density, OMEGA) to use enriched panels; removes direct DNA2PROTEINMAPPING call and delegates to ENRICHPANELS
subworkflows/local/enrichpanels/main.nf	New workflow that orchestrates DNA2PROTEINMAPPING and panel expansion for all panel types (all, prot, nonprot, synonymous, exons)
subworkflows/local/omega/main.nf	Removes inline panel expansion logic; now receives pre-enriched panels and subgenic region definitions from ENRICHPANELS workflow
subworkflows/local/createpanels/main.nf	Adds .first() calls to ensure single-file outputs for domains and postprocessed panels
modules/local/expand_regions/main.nf	Renames outputs from "hotspots" to "subgenic"; updates script to call add_subgenicregions.py instead of add_hotspots.py; fixes exons channel condition logic
modules/local/bbgtools/omega/preprocess/main.nf	Updates container to bbglab/omega:0.2.1; dynamically captures omega version at runtime
modules/local/bbgtools/omega/mutabilities/main.nf	Updates container to bbglab/omega:0.2.1; updates version reporting
modules/local/bbgtools/omega/estimator/main.nf	Updates container to bbglab/omega:0.2.1; changes label to cpu_medium; enables --cores parameter; removes deprecated impact groups; updates version reporting
conf/tmp_quick_fixes.config	Adds error handling for DNA2PROTEINMAPPING process with retry and ignore strategy
bin/omega_select_mutdensity.py	Filters out subgenic regions (containing "--") from gene mutation densities; removes else clause in error handling
bin/compute_mutdensity.py	Merges subgenic region annotations from enriched panels into mutation data for accurate mutation density calculation by region
bin/add_subgenicregions.py	Renames output files from "hotspots" to "subgenic"; improves panel name extraction logic

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[m-huertasp]

I think this is quite good job! I might be missing some context regarding where and why we are doing this but I added some comments. If you need any further help, feel free to let me know. I’d also maybe need you to explain the PR in more detail.😃

[FedericaBrando]

Given Marta's review I did a quick look on the code and it seems all correct. Running a linter every now and then helps with the deprecation errors - also, you can select nextflow version in the IDE to match the error and be sure that it doesn't break in prod.

Overall keep up the good work! 👊🏻