Add topic channels to Chromograph, DeepVariant, ExpansionHunter, and Stranger#9800
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ramprasadn merged 30 commits intonf-core:masterfrom Feb 4, 2026
Merged
Add topic channels to Chromograph, DeepVariant, ExpansionHunter, and Stranger#9800ramprasadn merged 30 commits intonf-core:masterfrom
ramprasadn merged 30 commits intonf-core:masterfrom
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ramprasadn
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mashehu
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modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap
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mashehu
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mashehu
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modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap
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@nf-core-bot fix linting |
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@nf-core-bot fix linting |
mashehu
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Feb 4, 2026
| { assert process.out.gvcf[0][0] == [id:'test', single_end:false] }, | ||
| { assert process.out.examples[0][1].size() == 4 }, | ||
| { assert snapshot( | ||
| process.out.examples[0][1].collect { file(it).name } |
| [ | ||
| "EXPANSIONHUNTER", | ||
| "expansionhunter", | ||
| "5.0.0]" |
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the ] at the end needs to be removed in all the versions for expansionhunter
| tuple val(meta), path("*.json.gz") , emit: json | ||
| tuple val(meta), path("*_realigned.bam") , emit: bam | ||
| path "versions.yml" , emit: versions | ||
| tuple val("${task.process}"), val('expansionhunter'), eval("ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//'"), topic: versions, emit: versions_expansionhunter |
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Suggested change
| tuple val("${task.process}"), val('expansionhunter'), eval("ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//'"), topic: versions, emit: versions_expansionhunter | |
| tuple val("${task.process}"), val('expansionhunter'), eval("ExpansionHunter --version 2>&1 | grep -m1 -oE '[0-9]+\.[0-9]+\.[0-9]+'"), topic: versions, emit: versions_expansionhunter |
shorter and fixes the additional bracket at the end
LouisLeNezet
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Feb 4, 2026
…Stranger (nf-core#9800) * add topics to chromograph * update deepvariant * update deepvariant * update expansionshunter * fix meta for rundeepvariant * lint checks * update snap * update env for exapansionhunter * update stranger * update stranger * update meta.yaml * update stranger eval * update tests * update test * add versions * [automated] Fix linting with Prettier * add version * simplify tests * modify test for makeexamples * [automated] Fix linting with Prettier * modify version capture expression --------- Co-authored-by: nf-core-bot <core@nf-co.re>
cavenel
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Feb 5, 2026
…Stranger (nf-core#9800) * add topics to chromograph * update deepvariant * update deepvariant * update expansionshunter * fix meta for rundeepvariant * lint checks * update snap * update env for exapansionhunter * update stranger * update stranger * update meta.yaml * update stranger eval * update tests * update test * add versions * [automated] Fix linting with Prettier * add version * simplify tests * modify test for makeexamples * [automated] Fix linting with Prettier * modify version capture expression --------- Co-authored-by: nf-core-bot <core@nf-co.re>
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PR checklist
Closes #XXX
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