Update Prokka version and fix gunzip alias#309
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Daniel-VM merged 10 commits intoJun 11, 2026
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Two issues fixed: 1. GUNZIP was invoked twice in the same workflow scope (prokka + bakta blocks). DSL2 prohibits duplicate process invocations. Added GUNZIP_BAKTA alias. 2. PROKKA module was updated to use topic channels for version reporting (emit: versions_prokka, topic: versions), but the workflow still referenced PROKKA.out.versions which no longer exists. Removed the stale reference since PROKKA now publishes versions via topic channel automatically. Fixes the error: No such property: versions for class: groovyx.gpars.dataflow.DataflowBroadcast
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Daniel-VM
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mashehu
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Jun 11, 2026
…ch docs recommendation
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Thanks @mashehu 🙌🏾 |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).PR Description
Update prokka and increase git nf-test volume limits to prevent git ci failure
(Related #306 )