Test and improve Nextflow pipeline: fix bugs, add stubs, add CI

[Copilot]

The Nextflow pipeline had broken CLI flags in modules/regions/main.nf, EXPORT_REGIONS was imported but never wired into the workflow, and there was no way to validate the pipeline DAG without containers or real data.

Bug fixes

• modules/regions/main.nf: removed nonexistent --workers flag; --table_regions → --table-regions; --tiledb_lb_typesumstat → --type_sumstat; output pattern was emitting locusbreaker filenames instead of region CSV output
• main.nf: added missing if (params.regions) block inside if (params.export) so EXPORT_REGIONS is actually invoked

Stub blocks

Added stub: blocks to all 8 modules (create_tiledb, ingestion, merge_metadata, snp, regions, locusbreaker, traits, recompute_meta), enabling DAG validation without containers:

nextflow run main.nf -profile test_ingest         -stub
nextflow run main.nf -profile test_export_snp     -stub
nextflow run main.nf -profile test_export_regions -stub
nextflow run main.nf -profile test_export_traits  -stub
nextflow run main.nf -profile test_export_lb      -stub
nextflow run main.nf -profile test_recompute_meta -stub

Test config (conf/test.config)

• test_recompute_meta: replaced hardcoded cluster paths with ${projectDir}/example_data/recompute_meta_test_table.csv
• test_export_traits: points to new trait_list_test.csv (correct TRAIT column format)
• test_export_regions: params aligned with fixed module

New example data files

File	Purpose
example_data/example_data_table_test.csv	Documents ingestion column format without cluster-specific paths
example_data/trait_list_test.csv	TRAIT column (Tgd:ENSG…) for traits export tests
example_data/recompute_meta_test_table.csv	CELL,CHR format for recompute-metadata tests

CI (.github/workflows/ci.yml)

Three jobs on every push/PR: Python pytest, Nextflow stub tests for all 6 profiles, and a full integration test that runs ingestion with -process.container null.

Docs

• docs/README.md: full rewrite — parameter tables for every workflow mode, module reference table, stub/integration testing guide
• README.md: added Nextflow testing section

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