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Bump version post 5.4
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
Update GTDB-Tk QC documentation to include CheckM and CheckM2
Re-add contigs vs scaffolds metaSPAdes selection
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Bump version for release v5.4.1
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jfy133
approved these changes
Mar 7, 2026
Update command to get python package versions in local modules
Update full test resources
Update help_text formatting for spades and megahit options
Update BUSCO and CheckM modules
famosab
approved these changes
Mar 12, 2026
famosab
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LGTM!
Just a few comments about the parameters :)
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| If the parameter `--save_checkm_reference` is set, additionally the used the CheckM reference datasets are stored in the output directory. | ||
| If the parameter `--save_checkm_data` is set, additionally the used the CheckM reference datasets are stored in the output directory. |
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You could add the parameter changes to the CHANGELOG in the future.
| </details> | ||
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| GUNC will be run if specified with `--run_gunc` as a standalone, unless CheckM is also activated via `--qc_tool 'checkm'`, in which case GUNC output will be merged with the CheckM output using `gunc merge_checkm`. | ||
| GUNC will be run if specified with `--run_gunc` as a standalone, unless CheckM is also activated via `--run_checkm`, in which case GUNC output will be merged with the CheckM output using `gunc merge_checkm`. |
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As above: add parameter changes to CHANGELOG :)
| ## A note on bin filtering | ||
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| The pipeline offers the ability to filter out bins that fall outside of a certain size in base pairs (`--bin_max_length`, `--bin_min_length`). | ||
| The pipeline offers the ability to filter out bins that fall outside of a certain size in base pairs (`--bin_max_size`, `--bin_min_size`). |
| }, | ||
| "SPLIT_FASTA": { | ||
| "biopython": "1.7.4", | ||
| "biopython": "1.74", |
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Was this a real version update -> then CHANGELOG? But I guess it was just incorrectly reported?
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Was incorrectly reported
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I don't see any of the updated README parameters here in the schema? SO I guess the docs where now updated after the params have been renamed some time ago? Then you can just ignore my remark about the CHANGELOG :)
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Exactly that, the docs were outdated / wrong
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Fixedlong_reads_platformin the input samplesheet (#985 by @vinisalazar)