Add new component: trtools_dumpstr#11848
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Pull request overview
Adds a new nf-core DSL2 module wrapping dumpSTR (TRTools) and includes nf-test coverage to validate expected outputs and version reporting.
Changes:
- Introduces
TRTOOLS_DUMPSTRmodule with optional filter-regions support andversionstopic emission. - Adds conda environment pinning (
trtools=6.1.0) and container selection for Docker/Singularity/Apptainer. - Adds nf-test workflow tests (including stub mode) and snapshots for expected outputs.
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/dumpstr/main.nf | New Nextflow module process implementing dumpSTR execution, outputs, and stub behavior |
| modules/nf-core/trtools/dumpstr/meta.yml | Module metadata (inputs/outputs/tool info/version topics) |
| modules/nf-core/trtools/dumpstr/environment.yml | Conda environment definition for TRTools |
| modules/nf-core/trtools/dumpstr/tests/main.nf.test | nf-test definitions invoking GangSTR then dumpSTR |
| modules/nf-core/trtools/dumpstr/tests/main.nf.test.snap | Stored snapshots for real + stub test assertions |
| modules/nf-core/trtools/dumpstr/tests/nextflow.config | Test-only process config (sets ext.prefix) |
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SPPearce
reviewed
Jun 7, 2026
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } |
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Suggested change
| { assert snapshot(process.out).match() } | |
| { assert snapshot(sanitizeOutput(process.out)).match() } |
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" |
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Suggested change
| def prefix = task.ext.prefix ?: "${meta.id}" | |
| def prefix = task.ext.prefix ?: "${meta.id}_dumpstr" |
| """ | ||
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| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" |
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| def prefix = task.ext.prefix ?: "${meta.id}" | |
| def prefix = task.ext.prefix ?: "${meta.id}_dumpstr" |
| --vcf $vcf \\ | ||
| --out $prefix \\ | ||
| --zip \\ | ||
| $optional_args |
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| $optional_args | |
| ${filter_regions_arg} \\ | |
| ${filter_regions_names_arg} \\ | |
| ${args} |
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| // Optional inputs | ||
| tuple path(filter_regions), path(filter_regions_tbi) | ||
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| // Optional inputs |
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| // Optional inputs |
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| def optional_args = [ | ||
| filter_regions_arg, | ||
| filter_regions_names_arg, | ||
| args | ||
| ].findAll { it } | ||
| .join(" ") |
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| def optional_args = [ | |
| filter_regions_arg, | |
| filter_regions_names_arg, | |
| args | |
| ].findAll { it } | |
| .join(" ") |
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| def region_files = filter_regions ? (filter_regions instanceof List ? filter_regions : [filter_regions]) : [] |
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Description of changes
This PR adds a new nf-core module for
dumpSTRfrom the TRTools package.PR checklist
Closes #11847
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda