Update mygene: topic versions, stub block, sanitizeOutput#11441
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HReed1 wants to merge 7 commits intonf-core:masterfrom
Open
Update mygene: topic versions, stub block, sanitizeOutput#11441HReed1 wants to merge 7 commits intonf-core:masterfrom
HReed1 wants to merge 7 commits intonf-core:masterfrom
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| tuple val(meta), path("*.gmt"), emit: gmt | ||
| tuple val(meta), path("*.tsv"), emit: tsv , optional: true | ||
| path "versions.yml" , emit: versions | ||
| path "versions.yml" , emit: versions_mygene, topic: versions |
mribeirodantas
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Apr 30, 2026
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mygene version is missing in teh snapshot file
…te snapshots - main.nf: rename emit: versions to emit: versions_mygene per nf-core convention - meta.yml: rename output key versions: to versions_mygene: to match emit name - tests/main.nf.test: update all assertions to process.out.versions_mygene[0] - tests/main.nf.test.snap: regenerate all 5 snapshots with versions_mygene channel Addresses review feedback from mribeirodantas on PR nf-core#11441.
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PR checklist
--profile docker,wavetests.nf-core modules lint).nf-test test).Description of changes
Migrates the mygene module to the nf-core v4.0.1 architecture:
path "versions.yml", topic: versionsemission. Note:mygeneuses a Pythontemplatescript, which prevents using theeval()tuple pattern (Nextflow blockseval()for non-Bash interpreters). The Python template generatesversions.ymlnatively, consistent withcellranger/count.stub:block that creates dummy output files and generatesversions.ymlvia bash.sanitizeOutput(process.out)per nf-test best practices.output: versions_mygeneandtopics: versionssections.Part of the v4.0.1 standardization effort tracked in #11323.
Part of #4570