Handle all python script inputs with click

[FerriolCalvet]

No description provided.

[Copilot]

Pull Request Overview

This PR updates all Python script invocations across the pipeline to use the Click command-line interface library instead of positional arguments, standardizing the command-line argument handling for better maintainability and user experience.

Key changes:

• Replaced positional arguments with named Click options for all Python scripts
• Removed TODO comments indicating the need for Click implementation
• Updated boolean flags to use proper Click flag syntax

Reviewed Changes

Copilot reviewed 10 out of 21 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
modules/local/writemaf/main.nf	Updated write_mafs.py to use --maf-file and --groups-json options
modules/local/sitesfrompositions/main.nf	Converted sites_table_from_positions.py to use named options and added cleanup command
modules/local/process_annotation/panelcustom/main.nf	Modified panel_custom_processing.py to use Click options and updated boolean flag handling
modules/local/process_annotation/mutations_custom/main.nf	Updated mutations_custom_processing.py to use named Click options
modules/local/group_genes/main.nf	Refactored features_2group_genes.py to use Click options with conditional argument handling
modules/local/filtermaf/main.nf	Converted filter_cohort.py to use descriptive Click option names
modules/local/dnds/preprocess/main.nf	Updated dNdS_preprocess.py to use Click options for file paths
modules/local/createpanels/sample/main.nf	Modified create_panel4sample.py to use Click options and updated TODO comment
modules/local/createpanels/captured/main.nf	Updated create_panel_versions.py to use Click options
modules/local/bbgtools/oncodrive3d/preprocessing/main.nf	Converted oncodrive3d_preprocessing.py to use Click options

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[m-huertasp]

I was just taking advantage that I was looking at the scripts to add those comments but they are not about the implementation of click.
The only script that I could find without click is check_samplesheet.py

[m-huertasp]

I've done some more tests, and I think everything is working fine! I have used a small pytest script for this -->
test_click.py