Update whamg: topic versions, stub block, sanitizeOutput#11450
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HReed1 wants to merge 4 commits intonf-core:masterfrom
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Update whamg: topic versions, stub block, sanitizeOutput#11450HReed1 wants to merge 4 commits intonf-core:masterfrom
HReed1 wants to merge 4 commits intonf-core:masterfrom
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SPPearce
requested changes
May 1, 2026
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| path(process.out.vcf[0][1]).vcf.summary, | ||
| file(process.out.tbi[0][1]).name, |
Contributor
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vcf and tbi files are typically unstable due to differences between conda/docker/singularity.
The vcf summary command comes from the nft-vcf plugin.
Any time you see a snapshot split out like this it means you need to take special care and not just snapshot the whole process.out.
You can use unstableKeys for the tbi channel, but the vcf summary is useful to keep for showing the vcf file is not changing.
| tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi | ||
| tuple val(meta), path("*.txt") , emit: graph, optional: true | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('whamg'), eval('whamg 2>&1 | grep Version | sed \'s/^Version: v//; s/-.*$//\''), topic: versions, emit: versions_whamg |
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Can you make this one sed command please.
- main.nf: emit: versions -> emit: versions_whamg - meta.yml: output key versions: -> versions_whamg: Local lint: 56/0. Local nf-test: 2/2 passed.
SPPearce
reviewed
May 4, 2026
| process.out.versions | ||
| ).match() | ||
| } | ||
| { assert snapshot(sanitizeOutput(process.out)).match() } |
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Still need to swap back to use nft-vcf for the vcf file, and the tbi is unstable
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PR checklist
--profile docker,wavetests.nf-core modules lint).nf-test test).Description of changes
Migrates the whamg module to the nf-core v4.0.1 architecture:
versions.ymlfile emission with dynamiceval()tuple emission on thetopic: versionschannel.stub:block for CI/CD stub-run support.sanitizeOutput(process.out)per nf-test best practices.output: versions_whamgandtopics: versionssections.Part of the v4.0.1 standardization effort tracked in #11323.
Part of #4570