New module for mergestr

[KondratievaOlesya]

This PR adds a new nf-core module for mergeSTR from the TRTools package.

PR checklist

Closes #12014

• 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
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[Copilot]

Pull request overview

Adds a new nf-core DSL2 module wrapping mergeSTR (TRTools) to merge multiple TR-genotyper VCFs into a single merged VCF, along with nf-test coverage.

Changes:

• Added trtools/mergestr module implementation (process, container/conda, outputs + versions topic).
• Added module metadata (meta.yml) and conda environment definition.
• Added nf-test tests, config overrides, and snapshots using gangstr-produced VCFs as inputs.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
modules/nf-core/trtools/mergestr/main.nf	Implements the TRTOOLS_MERGESTR process, including bgzip/tabix indexing and versions emission.
modules/nf-core/trtools/mergestr/meta.yml	Declares module inputs/outputs and version reporting metadata for nf-core tooling.
modules/nf-core/trtools/mergestr/environment.yml	Defines the conda environment (TRTools 6.1.0).
modules/nf-core/trtools/mergestr/tests/main.nf.test	Adds nf-test coverage (real + stub) for the new module.
modules/nf-core/trtools/mergestr/tests/main.nf.test.snap	Stores expected outputs for nf-test runs.
modules/nf-core/trtools/mergestr/tests/nextflow.config	Provides test-specific ext.args overrides for TRTOOLS_MERGESTR and the setup GANGSTR runs.

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