Address Nextflow linting, add param validation, reformatting

[dltamayo]

No description provided.

[github-actions]

Unit Test Results

10 tests   10 ✅  2m 44s ⏱️
 2 suites   0 💤
 1 files     0 ❌

Results for commit bfa4f50.

♻️ This comment has been updated with latest results.

[Copilot]

Pull request overview

This PR refactors the TCRtoolkit pipeline to improve code quality through linting compliance, centralized parameter validation, and modernized infrastructure. The changes introduce the nf-schema plugin for schema-based parameter validation, relocate configuration functions, remove redundant code, and optimize the Docker build process.

Key changes:

• Added JSON schema for parameter validation with the nf-schema plugin, replacing manual validation code
• Centralized container directives and relocated the check_max function to conf/base.config
• Refactored Python comparison calculations to eliminate dependencies and improve performance
• Optimized Dockerfile by switching to micromamba base image and consolidating build steps

Reviewed changes

Copilot reviewed 33 out of 35 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
workflows/tcrtoolkit.nf	Removed manual parameter validation code and added VALIDATE_PARAMS subworkflow call
subworkflows/local/validate_params.nf	New subworkflow that uses nf-schema plugin for parameter validation
nextflow_schema.json	New JSON schema defining all pipeline parameters with validation rules
nextflow.config	Added nf-schema plugin configuration and default parameter values
conf/base.config	Relocated check_max function from nextflow.config
conf/modules.config	Added centralized container directive for all processes
subworkflows/local/sample.nf	Improved lambda parameter naming for better code clarity
subworkflows/local/resolve_samplesheet.nf	Added samplesheet_utf8 input to SAMPLESHEET_RESOLVE and improved lambda naming
subworkflows/local/input_check.nf	Improved lambda parameter naming using underscore prefix for unused variable
modules/local/samplesheet/samplesheet_resolve.nf	Rewrote script using awk for improved row ordering and error handling
modules/local/samplesheet/samplesheet_check.nf	Removed process-level container directive
modules/local/sample/*.nf	Removed process-level container directives from multiple sample modules
modules/local/sample/tcrdist3.nf	Reformatted conditional expressions using ternary operators for conciseness
modules/local/compare/*.nf	Removed process-level container directives from compare modules
modules/local/airr_convert/*.nf	Removed process-level container directives from conversion modules
notebooks/*.qmd	Removed unused project_dir parameter from all notebook templates
bin/compare_calc.py	Refactored to inline similarity functions and optimize memory usage
bin/utils.py	Removed file as functions are now inlined in compare_calc.py
Dockerfile	Switched to micromamba base, optimized build layers, and improved cleanup
env.yml	Added r-grr=0.9.5 dependency
main.nf	Removed commented onComplete workflow section
LICENSE	Added MIT License file

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[dimalvovs]

lgtm!