general structure updates

[FerriolCalvet]

New version of the pipeline, containing:

• More extensive documentation (still not fully complete)
• Automated validation via nf-core plugin
• Passing all nextflow lint, but modules.config
• Update mutation rate to mutation density
• bug fixing

AI summary

This pull request introduces updates across several areas of the deepCSA project, including configuration changes, documentation enhancements, and code improvements. Key changes involve replacing "mutationrate" with "mutationdensity" in multiple configuration files, improving the README.md to provide clearer instructions and additional context, and refining the modules.config file to simplify and standardize prefixes for process outputs.

Configuration Updates:

• Replaced mutationrate with mutationdensity in multiple configuration files (conf/bladder.config, conf/chip.config, conf/chip_dwnsyndr.config, conf/chip_pancancer.config, conf/kidney.config, conf/kidney_bulk.config, conf/lung.config, conf/mice.config, conf/mice_mm10.config) to reflect a more accurate parameter naming convention. [1] [2] [3] [4] [5] [6] [7] [8] [9]

Documentation Enhancements:

• Updated README.md to include a new workflow overview image, clearer usage instructions, and a warning about parameter configuration. It also now includes a credits section listing contributors and a link to the documentation. [1] [2] [3] [4]
• Added a .markdownlint.json file to configure markdown linting rules, disabling MD013 and customizing MD024.

Code Improvements:

• Enhanced deepcsa_maf2samplevcfs.py script with detailed comments specifying mandatory columns for input mutations, improving usability and clarity.

Process Configuration Refinements:

• Simplified and standardized output prefixes in conf/modules.config by removing ${meta.id} references and using consistent naming conventions (e.g., .subset_depths, .all, .exons). These changes improve maintainability and readability. [1] [2] [3] [4] [5]
• Removed the ENSEMBLVEP_DOWNLOAD process configuration, indicating a cleanup of unused or redundant processes.

Other Changes:

• Fixed minor issues in conf/modules.config related to publish directory patterns and process configurations, ensuring consistency and correctness. [1] [2] [3] [4]

[Copilot]

Pull Request Overview

This PR updates the deepCSA pipeline to replace the “mutation rate” modules and parameters with “mutation density,” simplifies various process prefixes, removes the VEP cache download subworkflow, and enhances documentation/configuration for mutation density.

• Rename all mutationrate modules, channels, CLI flags, and configs to mutationdensity
• Remove the PREPARE_CACHE subworkflow and related VEP‐cache parameters
• Simplify module prefix logic and clean up unused imports

Reviewed Changes

Copilot reviewed 106 out of 122 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
workflows/deepcsa.nf	Swapped mutation rate modules for mutation density
nextflow_schema.json	Renamed mutationrate ➔ mutationdensity
nextflow.config	Added mutationdensity param; removed mutationrate
subworkflows/local/mutationdensity/main.nf	Introduced new mutation density subworkflow
modules/local/select_mutdensity/main.nf	Replaced SELECT_MUTRATES with SELECT_MUTDENSITIES
subworkflows/local/utils_nfcore_deepcsa/main.nf	Updated logo/citation helpers; removed purple blocks
conf/tools/mutdensity.config	Configured filters for mutation density processes

Comments suppressed due to low confidence (4)

subworkflows/local/mutationdensity/main.nf:1

• A new MUTATION_DENSITY subworkflow has been added; please add or update tests to cover its functionality and prevent regressions.

include { TABIX_BGZIPTABIX_QUERY    as SUBSETMUTATIONS      } from '../../../modules/nf-core/tabix/bgziptabixquery/main'

modules/local/select_mutdensity/main.nf:1

• The SELECT_MUTDENSITIES process replaces SELECT_MUTRATES; ensure you add corresponding tests to validate the new process logic.

process SELECT_MUTDENSITIES {

workflows/deepcsa.nf:7

• The imports for validateParameters, samplesheetToList, paramsHelp, and paramsSummaryLog were removed. Ensure any calls to those functions have also been removed or replaced to prevent missing-function errors at runtime.

include { paramsSummaryMap          } from 'plugin/nf-schema'

nextflow.config:64

• The signatures parameter is defined more than once in this block; remove the duplicate to avoid confusion or unintended overrides.

    signatures                  = false

[FerriolCalvet]

I am not sure if the review are required since you already accepted each of the branches that were merged here.
Let me know if you want to review or I just merge
@migrau @FedericaBrando

[FedericaBrando]

🚀

[migrau]

go ahead!