Test: expand test coverage for Docker, API, CLI subcommands, and various parameter combos

[berntpopp]

We need to broaden our test suite to ensure reliability and consistency across multiple areas of the project. The following tests should be added or expanded:

1. Docker Tests

   • Validate that running the pipeline or individual commands inside our Docker container works as expected.
   • Include at least one end-to-end test using Docker (e.g., mounting local data, running a pipeline command, verifying output).

2. API Tests

   • If we have an API layer, confirm endpoint functionality (e.g., job submission, status checking, result retrieval).
   • Ensure JSON responses, error handling, and edge cases are tested.

3. CLI Tests with adVNTR

   • Confirm that --extra-modules advntr works correctly.
   • Verify that relevant output files (e.g., output_adVNTR_result.tsv) are generated.
   • Test new or existing parameters for the adVNTR module (e.g., --advntr-max-coverage).

4. Subcommand Tests

   • Cover each subcommand (pipeline, report, cohort, online, etc.) with at least one basic run-through.
   • Test optional arguments (e.g., --keep-intermediates, --archive-results) to confirm files are retained or removed as expected.

5. Parameter Combinations

   • Run tests that toggle various flags: --keep-intermediates, --delete-intermediates, --fast-mode, etc.
   • Confirm that the required files are present or deleted after each run, depending on the parameters.

6. Additional FASTQ Cases

   • Add a second FASTQ example to confirm robust handling.
   • Include a FASTQ test without the Shark module (e.g., no --extra-modules shark) to confirm the pipeline still runs normally.

Acceptance Criteria:

1. Docker

   • At least one test that builds/pulls the Docker image, runs the pipeline, and verifies success.

2. API

   • Confirm endpoints respond with correct statuses, handle invalid inputs gracefully, and generate valid JSON outputs.

3. CLI + adVNTR

   • A test scenario that runs vntyper pipeline --extra-modules advntr with a known input and verifies correct adVNTR output.

4. Subcommands

   • Each subcommand (pipeline, report, cohort, online) has at least one passing test scenario.

5. Parameter Matrix

   • Tests that toggle various command-line arguments and confirm the presence or absence of intermediate or final files.

6. Additional FASTQ Scenarios

   • At least one new test using an alternate FastQ dataset.
   • Confirm pipeline runs fine with no Shark filtering if --extra-modules shark is omitted.