Update GTDB-Tk QC documentation to include CheckM and CheckM2#984
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dialvarezs merged 5 commits intodevfrom Mar 2, 2026
Merged
Update GTDB-Tk QC documentation to include CheckM and CheckM2#984dialvarezs merged 5 commits intodevfrom
dialvarezs merged 5 commits intodevfrom
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Release 5.4.0 (Yellow Frog)
The `gtdbtk_min_completeness` and `gtdbtk_max_contamination` parameters previously described filtering as applying only to BUSCO quality metrics. However, since v2.5 the pipeline supports multiple bin QC tools (BUSCO, CheckM, CheckM2) and the filter applies to results from any/all of them. Update help_text in nextflow_schema.json and descriptions in docs/output.md to accurately reflect that completeness and contamination filtering works across all available bin QC tools, not exclusively BUSCO. Fixes #983 https://claude.ai/code/session_01GFjgJHCGv7Jn9ZEdsVMv8p
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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: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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jfy133
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Mar 2, 2026
prototaxites
reviewed
Mar 2, 2026
| "default": 10, | ||
| "description": "Max. bin contamination (in %) allowed to apply GTDB-tk classification.", | ||
| "help_text": "Contamination approximated based on BUSCO analysis (%Complete and duplicated). If too high, GTDB-tk classification results can be impaired due to contamination!", | ||
| "help_text": "Contamination assessed with any of the bin QC tools (BUSCO, CheckM, CheckM2). The minimum contamination value across all available QC tools is used for filtering. If too high, GTDB-tk classification results can be impaired due to contamination!", |
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Just want to double check that this is an accurate representation of the code? I think the code applies the filter to all value pairs from all tools and passes the bin if any pair passes, is that equivalent to these descriptions?
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Yes, you're right, I'm going to rephrase it. But I guess the effect is actually the same.
mag/subworkflows/local/gtdbtk/main.nf
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Description
This PR updates the documentation and schema to clarify that GTDB-Tk bin quality filtering now supports multiple QC tools beyond BUSCO, including CheckM and CheckM2.
PR Checklist
docs/output.mdis updatednextflow_schema.jsonis updatedhttps://claude.ai/code/session_01GFjgJHCGv7Jn9ZEdsVMv8p
Closes #983.