Cleanup params

[julianu]

Definition of params into config file, usage of schema

[Copilot]

Pull Request Overview

This PR centralizes parameter definitions from individual Nextflow module files into a global configuration file and implements a schema for parameter validation. The changes move hardcoded container references and parameter definitions to enable better configuration management and consistency across the pipeline.

• Move all parameter definitions from individual .nf files to nextflow.config for centralized management
• Replace hardcoded container references with labels and implement container mapping in the docker profile
• Add comprehensive nextflow_schema.json for parameter validation and documentation
• Remove redundant nextflow.enable.dsl=2 declarations throughout modules

Reviewed Changes

Copilot reviewed 17 out of 19 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
nextflow.config	Centralizes all pipeline parameters and implements container label mapping
nextflow_schema.json	Adds comprehensive parameter validation schema
main.nf	Removes duplicated parameter definitions
src/preprocess/create_entrapment_database.nf	Updates container reference to use labels and adds memory parameter
src/preprocess/create_decoy_database.nf	Removes parameter definitions and updates container reference
src/preprocess/convert_to_mzml.nf	Removes parameter definitions and updates container references
src/postprocessing/*.nf	Removes parameter definitions and updates container references to use labels
src/identification/*.nf	Removes parameter definitions and updates container references to use labels

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