Improve handling of GTDB-Tk + Bin QC #954
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dialvarezs merged 4 commits intonf-core:devfrom Dec 3, 2025
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🤔 I think this might be fine as a temporary fix, if we want to squeak this in before the next release and fix the bug in the moment. But IMO GTDB-Tk should execute on /all/ bins if no BinQC tool is specified - even if they're low quality. It's already possible to set the GTDB QC thresholds to 0% completeness, 100% contamination anyway, even if you run a BinQC tool. |
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I guess you're right @prototaxites, let's go with this for now and then we can run GTDB-Tk on all bins if QC is disabled. |
prototaxites
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Dec 3, 2025
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This adds a warning message when no Bin QC tool is enabled and GTDB-Tk is.
It also prevent GTDB-Tk actually running when Bin QC is disabled or no QC tool is enabled.
Reported in slack: https://nfcore.slack.com/archives/CE9MS66BS/p1764749516249169
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).