init workflow level tests

[dimalvovs]

This pull request refactors the BULKTCR_ANALYSIS workflow in bulktcr_analysis.nf to improve maintainability and clarity by centralizing channel assignments, streamlining report generation, and updating test definitions for better reuse. The changes reduce code duplication, make channel management more explicit, and simplify test configuration.

Workflow refactoring and channel management:

• Centralized the creation and assignment of all output channels (e.g., ch_sample_csv, ch_tcrdist_files, ch_giana_files, etc.) at the start of the workflow, and used these consistently throughout, replacing scattered conditional assignments. [1] [2]
• Updated all report generation logic to use the new centralized channels, improving consistency and reducing repeated code for handling outputs at different analysis levels (sample, patient, compare). [1] [2] [3] [4]

Report logic improvements:

• Refactored the mixing and staging of report files to use the new channels, clarified the inclusion of files for each report type, and improved the logic for handling different analysis levels. [1] [2] [3] [4]

Testing improvements:

• Updated test configuration in tests/main.nf.test to define the container image and integration modes at the top, and reused these variables in all test cases, reducing duplication and improving maintainability. [1] [2] [3] [4]

[github-actions]

Unit Test Results

17 tests  ±0   17 ✅ ±0   7m 13s ⏱️ - 1m 0s
 7 suites ±0    0 💤 ±0 
 1 files   ±0    0 ❌ ±0 

Results for commit 89cf8a6. ± Comparison against base commit 5adb53c.

♻️ This comment has been updated with latest results.

[dltamayo]

LGTM