Integrity tests: Review normal test, add omega test and include documentation.

[migrau]

[generatd by copilot]

This pull request adds support for using a precomputed depths table in the DEEPCSA pipeline, allowing users to skip depth calculation from BAM files and provide their own table for downstream analysis. It also introduces a minimal test suite using nf-test to validate pipeline runs and outputs. The most important changes are grouped below.

Custom Depths Table Feature

• Added use_custom_depths and custom_depths_table parameters to nextflow.config, enabling users to specify a precomputed depths table for the pipeline instead of computing depths from BAM files.
• Updated the depth analysis subworkflow (subworkflows/local/depthanalysis/main.nf) to conditionally use the provided depths table when use_custom_depths is true, bypassing the depth computation process.
• Documented the new feature in docs/usage.md, including instructions, requirements, and notes on preparing the input table.
• Extended the pipeline schema (nextflow_schema.json) to describe the new parameters and their expected usage, improving configuration clarity and validation.

Testing Infrastructure

• Added a minimal reproducible test suite using nf-test: includes two test cases (minimal run and omega analysis), snapshot validation, and documentation for running and updating tests. (tests/README.md, tests/deepcsa.nf.test, tests/deepcsa.nf.test.snap, [1] [2] [3] [4]
• Provided a small test input dataset in tests/test_data/input.csv for use in automated testing.

These changes improve pipeline flexibility and reproducibility, making it easier for users to re-use depth calculations and for developers to validate pipeline outputs with automated tests.

[Copilot]

Pull Request Overview

This pull request adds two significant features to the DEEPCSA pipeline: support for using precomputed depths tables (bypassing BAM depth calculation) and a minimal nf-test suite for automated testing. The changes improve pipeline flexibility by allowing users to reuse depth calculations and establish a foundation for reproducible testing.

• Added use_custom_depths and custom_depths_table parameters to enable skipping depth computation
• Introduced nf-test-based test infrastructure with two test cases (minimal and omega analysis)
• Updated documentation to explain the custom depths feature and test suite usage

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
nextflow.config	Added two new parameters for custom depths table feature
nextflow_schema.json	Extended schema with custom depths table options and validation rules
subworkflows/local/depthanalysis/main.nf	Implemented conditional logic to use custom depths or compute from BAMs
docs/usage.md	Documented the custom depths table feature with usage instructions
tests/deepcsa.nf.test	Defined two nf-test cases with assertions for pipeline validation
tests/deepcsa.nf.test.snap	Snapshot file for deterministic output validation
tests/README.md	Comprehensive documentation for running and maintaining tests
tests/nextflow.config	Test-specific configuration with pipeline parameters
tests/test_data/input.csv	Test input dataset with sample metadata
nf-test.config	nf-test framework configuration
assets/useful_scripts/downsample_depths.ipynb	Helper notebook for preparing custom depths tables

Comments suppressed due to low confidence (1)

tests/deepcsa.nf.test:59

• The line count assertion lines.size() == 59 is fragile and will break if the test data changes. Consider checking lines.size() > 1 (has header + data) or use a more flexible approach that validates the structure rather than an exact count.

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[migrau]

Most of copilot comments are related to the Custom Depths Table Feature part, so feel free to review them @FerriolCalvet.
I mistakenly did a commit amend, so that's why it is merging the previous commit with my current one.
Anyway, it is going to be merge to dev now.

[FerriolCalvet]

looks good!