New module for mergestr#12015
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KondratievaOlesya merged 7 commits intoJul 2, 2026
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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/mergestrmodule 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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LouisLeNezet
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Jul 1, 2026
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Just a few comments but good to go otherwise
LouisLeNezet
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Jul 1, 2026
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name + ":variantsMD5," + path(it).vcf.variantsMD5 }}, |
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This is really nice, we often just do path(process.out.vcf[0][1]).vcf.variantsMD5 but this does work.
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Thank you for the review! |
vagkaratzas
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Jul 2, 2026
* New module for mergestr * Fix review * Fix typo in stub * Fix typo in stub * Fix review comments
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This PR adds a new nf-core module for
mergeSTRfrom the TRTools package.PR checklist
Closes #12014
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda