Add REGENIE step1 and step2 modules with Wave containers and expanded GWAS tests

[lyh970817]

This PR adds regenie/step1 and regenie/step2 with Wave-backed containers and GWAS-focused tests covering quantitative and binary phenotypes, covariates, and step2 consumption of setup-generated step1 predictions. The shared test data needed for these tests is now merged upstream in nf-core/test-datasets#1919.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions - See version_topics
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

[Copilot]

Pull request overview

Adds new nf-core module implementations for running REGENIE GWAS in two stages (step1 model fitting and step2 association testing), including Wave-backed containers and nf-test coverage for quantitative/binary phenotypes with covariates and step2 consumption of step1 predictions.

Changes:

• Introduce regenie/step1 and regenie/step2 modules (Nextflow process, meta.yml, conda env, Wave containers).
• Add nf-test suites + snapshots for quantitative/binary PLINK1 runs with covariates, plus stubbed PLINK2 scenarios.
• Add per-test modules_testdata_base_path config to use upstream module test datasets.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
modules/nf-core/regenie/step1/main.nf	Implements REGENIE step1 process emitting prediction list + LOCO files
modules/nf-core/regenie/step1/meta.yml	Declares step1 module I/O contract, containers, and versions topic
modules/nf-core/regenie/step1/environment.yml	Conda environment for REGENIE 4.1.2
modules/nf-core/regenie/step1/tests/main.nf.test	nf-test cases for quantitative/binary + stub mode
modules/nf-core/regenie/step1/tests/main.nf.test.snap	Snapshot expectations for step1 tests
modules/nf-core/regenie/step1/tests/nextflow.config	Testdata base path configuration
modules/nf-core/regenie/step2/main.nf	Implements REGENIE step2 association testing consuming step1 predictions
modules/nf-core/regenie/step2/meta.yml	Declares step2 module I/O contract, containers, and versions topic
modules/nf-core/regenie/step2/environment.yml	Conda environment for REGENIE 4.1.2
modules/nf-core/regenie/step2/tests/main.nf.test	nf-test cases validating step2 with step1-produced predictions + stub mode
modules/nf-core/regenie/step2/tests/main.nf.test.snap	Snapshot expectations for step2 tests
modules/nf-core/regenie/step2/tests/nextflow.config	Testdata base path configuration

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