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dialvarezs merged 2 commits into from
Jul 16, 2026
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docs: update BUSCO output docs after excluding complete directory #1075

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34485eb
docs: remove unpublished BUSCO complete directory from output docs
dialvarezs Jul 15, 2026
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chore: fill PR number in changelog
dialvarezs Jul 15, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1070](https://github.com/nf-core/mag/pull/1070) - Update BUSCO nf-core module (by @dialvarezs)
- [#1071](https://github.com/nf-core/mag/pull/1071) - Improved efficiency by batching `DASTOOL_FASTATOCONTIG2BIN` per binner instead of per bin (by @dialvarezs)
- [#1074](https://github.com/nf-core/mag/pull/1074) - Exclude BUSCO output directories to reduce storage usage in output dir (by @dialvarezs)
- [#1075](https://github.com/nf-core/mag/pull/1075) - Update output documentation to reflect BUSCO complete directory no longer being published (by @dialvarezs)

### `Fixed`

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9 changes: 0 additions & 9 deletions docs/output.md
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Expand Up @@ -636,18 +636,9 @@ If a lineage dataset is specified already with `--busco_db`, only results for th
- `[sample/group]-[lineage]-busco.batch_summary.txt`: Summary table of the BUSCO results for the bins in the sample.
- `short_summary.generic.[lineage].[assembler]-[bin].{txt,json}`: A detailed BUSCO summary for each bin, available in both plain text and JSON format.
- `[sample/group]-[lineage]-busco.log`: Log file of the BUSCO run.
- `[assembler]-[bin]/`
- `prodigal_output/predicted_genes/predicted.{fna,faa}`: Predicted genes by Prodigal in FASTA format.
- `logs/`: Logs for each of the tools used by BUSCO.
- `run-[specific_lineage]:`
- `full_table.tsv`: A detailed table indicating the complete BUSCO gene list for the lineage, detailing their presence in the assembly.
- `missing_busco_list.tsv`: List of BUSCOs that were not found in the assembly.
- `busco_sequences/*/*.{fna,faa}`: Nucleotide and aminoacid sequences of all identified BUSCOs (single copy, multi copy and fragmented).

</details>

If the parameter `busco_clean` is set to `false`, the BUSCO directory will preserve additional files, including outputs from the tools BUSCO utilizes and the `auto_lineage/` directory. This directory contains results for each lineage tested during automated lineage selection.

If the parameter `--save_busco_db` is set, additionally the used BUSCO lineage datasets are stored in the output directory.

<details markdown="1">
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