Fix warnings, clean namings and overall improvement

[FerriolCalvet]

AI summary

This pull request introduces several significant changes to the pipeline's configuration and output management, focusing on improved organization of output files, clearer parameter naming, and enhanced maintainability. The most important updates include a comprehensive reorganization of output directories, renaming and consolidation of process parameters, and the addition of a dedicated configuration file for result outputs.

Output Directory and Process Organization:

• Output directories for many processes have been standardized and reorganized to use clearer, more descriptive paths (e.g., moving outputs into processing_files, mutations, plots, qc, etc.) to improve discoverability and maintainability. (conf/modules.config [1] [2] [3] [4] [5] [6]
• A new configuration file, results_outputs.config, was added to centralize and fine-tune the output locations and patterns for plots, QC, and annotation steps, further enhancing output consistency. (conf/results_outputs.config [1] conf/modules.config [2]

Process and Parameter Refactoring:

• Several process names and parameters were renamed for clarity and consistency, such as changing SUBSET* processes to QUERY*, and updating parameters like omega_withingene to create_subgenic_regions. (conf/modules.config [1] [2] [3] [4] [5]
• Deprecated or redundant configuration files and parameters were removed, including the deletion of conf/general_files_BBG.config. (conf/general_files_BBG.config conf/general_files_BBG.configL1-L28)

Schema and Documentation Updates:

• Improved error messages for input schema fields to be more descriptive and user-friendly, and updated required fields for sample input. (assets/schema_input.json assets/schema_input.jsonL28-R36)
• Enhanced script documentation with clearer usage examples and references to input data sources. (assets/useful_scripts/signatures_sigprofilerextractor.py assets/useful_scripts/signatures_sigprofilerextractor.pyL38-R40)

Other Notable Changes:

• Adjusted publishDir settings for specific processes to disable output where appropriate or to refine file patterns and save logic. (conf/modules.config [1] [2]
• Minor logic tweaks, such as removal of unnecessary filter assignments. (conf/modules.config conf/modules.configL253)

These changes collectively improve the clarity, usability, and maintainability of the pipeline's configuration and outputs.

[Copilot]

Pull request overview

This pull request implements a comprehensive refactoring focused on parameter standardization, process renaming, and workflow improvements. The changes replace omega_* prefixed parameters with more general subgenic_* naming, rename SUBSET* processes to QUERY* for clarity, and standardize channel factory methods from Channel to lowercase channel. Additionally, the PR introduces optional BAM file requirements, adds new QC plotting capabilities, and reorganizes output publishing through a new configuration file.

Changes:

• Standardized parameter names from omega_withingene, omega_autodomains, omega_autoexons, omega_subgenic_bedfile to create_subgenic_regions, autodomains, autoexons, subgenic_bedfile across all configuration files, workflows, modules, and documentation
• Renamed processes from SUBSET* to QUERY* (e.g., SUBSETMUTATIONS → QUERYMUTATIONS) for better semantic clarity
• Standardized channel factory methods from Channel to lowercase channel throughout the codebase
• Made BAM files optional in the input samplesheet when using custom depths, with corresponding validation updates
• Added new results_outputs.config for centralized output directory management and PLOTTINGQC subworkflow with omega QC filtering
• Updated default parameter values including consensus_panel_min_depth (500→200), mutation_depth_threshold (40→100), and hotspot_expansion (30→0)

Reviewed changes

Copilot reviewed 44 out of 52 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Updated process names (SUBSET→QUERY, SYNMUTREADSRATE→SYNMUTREADSDENSITY), channel factory standardization, BAM handling logic, and PLOTTINGQC integration
subworkflows/local/*.nf	Consistent renaming of SUBSET to QUERY processes, channel factory standardization, removal of unnecessary .first() calls on process outputs
modules/local/expand_regions/main.nf	Updated parameter references from omega_* to standardized names
nextflow.config	Renamed parameters, reordered filter criteria, updated default thresholds for depth and mutation filtering
nextflow_schema.json	Updated schema with new parameter names, descriptions, and reorganized options sections
conf/tools/*.config	Updated process names and added publish directories for expanded regions outputs
conf/results_outputs.config	New file centralizing output publication paths for plots and QC processes
bin/*.py	Updated mutation density metric names (MUTREADSRATE→MUTREADSDENSITY), added omega flagging support, improved BAM column handling
docs/*.md	Updated documentation to reflect new parameter names and process changes
subworkflows/nf-core/utils_*.nf	Channel factory standardization and function name updates

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[FerriolCalvet]

update filter to flag

[Copilot]

Pull request overview

Copilot reviewed 53 out of 71 changed files in this pull request and generated 5 comments.

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[m-huertasp]

I really like the changes you've added (which are quite a lot). I've been adding some minor coments and I've tested some things, everything looks quite good!

There are more warnings about the .first() thing than before, I've been checking and I still don't understand why or how to solve them all without crashing something.

If you want we can discuss about an coment!

[FerriolCalvet]

thanks for the comments and testing things Marta!!

I am merging it and let's add you changes and we will see if there is any corner case that we missed to test