Feature/add unit test scaffolding

[hweej]

1. Adds initial unit test scaffolding for SAMPLESHEET_CHECK and CONVERT_ADAPTIVE nextflow processes.
2. Also modifies the github actions workflow to run unit tests before the integration test. Since running the pipeline even on the minimal-example takes quite some time before it might fail.
3. Adds smaller bite-sized testing fixtures to use per-process

Once the scaffolding is set up we can write some unit tests for #60

[github-actions]

Unit Test Results

10 tests   10 ✅  2m 50s ⏱️
 2 suites   0 💤
 1 files     0 ❌

Results for commit f514062.

♻️ This comment has been updated with latest results.

[Copilot]

Pull Request Overview

This PR introduces comprehensive test infrastructure using nf-test for the Nextflow pipeline. The changes add unit tests for core modules (SAMPLESHEET_CHECK and CONVERT_ADAPTIVE), create test fixtures with sample data, and enhance the CI/CD workflow to run automated tests on pull requests.

Key changes:

• Adds nf-test unit tests for samplesheet validation and Adaptive format conversion modules
• Creates test fixtures including valid, empty, malformed, and missing-column samplesheets, plus Adaptive TCR data files
• Restructures GitHub Actions workflow to run separate unit tests and pipeline integration tests with JUnit XML reporting

Reviewed Changes

Copilot reviewed 12 out of 13 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/modules/local/samplesheet/samplesheet_check.nf.test	Unit tests for samplesheet validation covering valid, empty, malformed, and minimal-example inputs
tests/modules/local/airr_convert/convert_adaptive.nf.test	Unit tests for Adaptive format conversion including metadata preservation, gene call validation, and error handling
tests/fixtures/valid_samplesheet.csv	Test fixture with valid 4-sample samplesheet data
tests/fixtures/empty_samplesheet.csv	Test fixture with header-only samplesheet for edge case testing
tests/fixtures/malformed_samplesheet.csv	Test fixture with malformed CSV data for error handling validation
tests/fixtures/missing_columns_samplesheet.csv	Test fixture missing required columns for validation testing
tests/fixtures/data/PD1_Patient*.tsv	Test fixtures with Adaptive TCR format data subsets for conversion testing
tests/fixtures/data/malformed_adaptive.tsv	Malformed Adaptive data for error handling tests
.gitignore	Adds nf-test artifacts and output directories to ignore list
.github/workflows/nextflow-test.yaml	Refactored CI workflow with separate unit-tests and pipeline-test jobs, adds test result publishing and artifact uploading

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[Copilot]

The pipeline-test job generates pipeline-test-results.xml but doesn't have steps to publish or upload these results, unlike the unit-tests job (lines 39-53). Consider adding similar steps to publish and upload the pipeline test results for consistency and better CI/CD visibility.

Suggested change

	run: nf-test test tests/main.nf.test --verbose --junitxml=pipeline-test-results.xml
	run: nf-test test tests/main.nf.test --verbose --junitxml=pipeline-test-results.xml
	- name: Publish pipeline test results
	if: always()
	uses: EnricoMi/publish-unit-test-result-action@v2
	with:
	files: pipeline-test-results.xml
	check_name: Pipeline Test Results
	- name: Upload pipeline test results
	if: always()
	uses: actions/upload-artifact@v4
	with:
	name: pipeline-test-results
	path: |
	.nf-test/tests/
	pipeline-test-results.xml

[hweej]

We would normally keep the --junitxml resulting artifact from Integration like tests. So in the ideal scenario we should keep this option. BUT, the integration tests here use a relatively large dataset, so the resulting artifact generated by the tests is quite large. Gigabytes in size IIRC.

The correct solution is to use a dataset that is a bit more truncated that the one in the minimal-example

[dimalvovs]

Nice work on adding module tests!

There is one copilot comment that looks legit, should we accept proposed changes?