Add CellRanger multi support for GEX+VDJ (tested case: gex + vdj-t + vdj-b)

[glrs]

This pull request includes several changes to improve the robustness and functionality of the run_sample.py script in the lib/realms/tenx directory. The changes focus on ensuring default values for configurations, refining the generation of required files, and enhancing the command assembly logic.

Improvements to Default Values and Initialization:

• lib/realms/tenx/run_sample.py: Modified the __init__ method to set default empty dictionaries for project_info, config, and reference_genomes if they are not provided. [1] [2]
• lib/realms/tenx/run_sample.py: Updated the collect_reference_genomes method to handle cases where config might be None.

Enhancements to File Generation:

• lib/realms/tenx/run_sample.py: Refined the process method to dynamically generate required files based on a files_to_generate configuration.
• lib/realms/tenx/run_sample.py: Split the generate_libraries_csv method into collect_libraries_data and generate_libraries_csv for better modularity and ensured directory creation before file writing. collect_libraries_data also used in generate_multi_sample_csv.
• lib/realms/tenx/run_sample.py: Implemented the generate_multi_sample_csv method to generate the multi-sample CSV file based on pipeline information and configuration.

Command Assembly Logic:

• lib/realms/tenx/run_sample.py: Improved the assemble_cellranger_command method by logging pipeline details, handling missing required arguments, and ensuring the output directory argument is always included. [1] [2]

Minor Logging Adjustments:

• lib/realms/tenx/tenx_project.py: Removed redundant logging of lab samples in the extract_samples method.