add test setup and first tests

[FerriolCalvet]

initialization of nextflow tests with nf-test.

• defining basic test for the entire pipeline
• define test for specific process as well (EXPANDREGIONS)

[Copilot]

Pull Request Overview

This PR initializes test infrastructure for the DEEPCSA pipeline using nf-test framework. It sets up the testing environment and adds basic tests for both the entire pipeline and specific processes.

• Sets up nf-test configuration and test directory structure
• Adds pipeline-level tests with various parameter combinations (mostly commented out)
• Implements specific process tests for the EXPAND_REGIONS module
• Includes test data files and configurations for different execution environments

Reviewed Changes

Copilot reviewed 11 out of 14 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
workflows/tests/deepcsa.nf.test	Pipeline-level test definitions with minimal features test
tests/nextflow.config	Test-specific Nextflow configuration with cluster and Singularity settings
tests/main.nf.test	Basic workflow test template
test_data/modules/*.bed	Test data files for module testing
nf-test.config	Main nf-test configuration file
modules/local/expand_regions/tests/main.nf.test*	Process-specific tests and snapshots for EXPAND_REGIONS
modules/local/expand_regions/main.nf	Updated stub section for testing
conf/test.config	Simplified test profile configuration
conf/local.config	Updated local execution configuration

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

[FerriolCalvet]

Fede I asked for your review in case you have some general comments about the testing set up or something important to take into account that I overlooked.

For now I want to merge this so that the first tests are implemented in dev even if the size of the tests and some of the data cannot be fully shared, but I have a batch of data ready to add for testing that is much smaller and can be publicly shared.
(see this run in Seqera: https://cloud.seqera.io/orgs/bbglabirb/workspaces/Prominent/watch/5jzs5up9XeLKdC/v2/tasks)

I would be happy to receive any feedback you can provide and I am debating how to store the data

[FerriolCalvet]

Is it realistic to upload this as tests in this repo?

$ l /data/bbg/nobackup2/scratch/fcalvet/fetch_duplex_fastqs/2025-09-21_deepUMIcaller/sortbamduplexcons/
total 283M
-rw-rw---- 1 bbgseqera nlopezb_g 22M Sep 20 22:03 B11.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 118 Sep 20 22:03 B11.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 14M Sep 20 22:00 B12.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 193 Sep 20 22:00 B12.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 19M Sep 20 21:53 B10.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 152 Sep 20 21:53 B10.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 24M Sep 20 21:52 B9.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 118 Sep 20 21:52 B9.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 30M Sep 20 21:49 B5.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 118 Sep 20 21:49 B5.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 19M Sep 20 21:41 B7.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 155 Sep 20 21:41 B7.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 18M Sep 20 21:38 B1.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 229 Sep 20 21:38 B1.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 21M Sep 20 21:37 B6.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 157 Sep 20 21:37 B6.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 27M Sep 20 21:37 B4b.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 11M Sep 20 21:37 B3.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 135 Sep 20 21:37 B3.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 139 Sep 20 21:37 B4b.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 13M Sep 20 21:35 B8.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 118 Sep 20 21:35 B8.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 21M Sep 20 21:34 B13.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 135 Sep 20 21:34 B13.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 25M Sep 20 21:30 B4a.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 137 Sep 20 21:30 B4a.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 13M Sep 20 21:25 B2a.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 137 Sep 20 21:25 B2a.sorted.bam.csi
-rw-rw---- 1 bbgseqera nlopezb_g 13M Sep 20 21:25 B2b.sorted.bam
-rw-rw---- 1 bbgseqera nlopezb_g 151 Sep 20 21:25 B2b.sorted.bam.csi

[FedericaBrando]

Overall if the test run as expected then the implementation is fine, I added some minor comments on some doubts that I had when reading the code and also some advice on commented code, pandas copy().

Your choice if you want to address them or not, if you confirm that tests work then it can be merged.

🚀

[FedericaBrando]

here I advise to use panel_data.copy(), slicing on a view of a df may give weird results

[FerriolCalvet]

first version of tests work and I am merging it.
There are still several pending tasks related to tests: adding full test data, increasing test coverage, ...

[FerriolCalvet]

pending things listed above