Update salsa2: topic versions, stub block, sanitizeOutput#11445
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HReed1 wants to merge 4 commits intonf-core:masterfrom
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Update salsa2: topic versions, stub block, sanitizeOutput#11445HReed1 wants to merge 4 commits intonf-core:masterfrom
HReed1 wants to merge 4 commits intonf-core:masterfrom
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SPPearce
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May 1, 2026
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Use val when explicitly setting a version string, not eval.
| tuple val(meta), path("*_scaffolds_FINAL.agp") , emit: agp | ||
| tuple val(meta), path("*/*scaffolds_FINAL.original-coordinates.agp"), emit: agp_original_coordinates, optional: true | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('salsa2'), eval("echo 2.3"), topic: versions, emit: versions_salsa2 |
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| tuple val("${task.process}"), val('salsa2'), eval("echo 2.3"), topic: versions, emit: versions_salsa2 | |
| tuple val("${task.process}"), val('salsa2'), val("2.3"), topic: versions, emit: versions_salsa2 |
- main.nf: emit: versions -> emit: versions_salsa2 - meta.yml: output key versions: -> versions_salsa2: - tests/main.nf.test.snap: regenerate snapshots Local lint: 53/0. Local nf-test: 2/2 passed.
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PR checklist
--profile docker,wavetests.nf-core modules lint).nf-test test).Description of changes
Migrates the salsa2 module to the nf-core v4.0.1 architecture:
versions.ymlemission with dynamiceval()tuple emission on thetopic: versionschannel. Note:salsa2does not expose a CLI version flag, so the version is hardcoded viaeval("echo 2.3")— consistent with existing upstream convention.stub:block for CI/CD stub-run support.sanitizeOutput(process.out)per nf-test best practices.output: versions_salsa2andtopics: versionssections.Part of the v4.0.1 standardization effort tracked in #11323.
Part of #4570