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Fix BUSCO and TIARA report concatenation#943

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dialvarezs merged 7 commits intonf-core:devfrom
dialvarezs:fix-busco-concat
Nov 28, 2025
Merged

Fix BUSCO and TIARA report concatenation#943
dialvarezs merged 7 commits intonf-core:devfrom
dialvarezs:fix-busco-concat

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@dialvarezs dialvarezs commented Nov 27, 2025

This PR replaces csvtk/concat with qsv/cat, which provides a “smart” column-aware concatenation. This allows the pipeline to concatenate CSV/TSV files with uneven columns, an issue that happens with BUSCO sometimes, as reported in #871.

This PR also fixes the creation of the Tiara report channel used for concatenation, an issue we’ve seen recently and which was reported on Slack: https://nfcore.slack.com/archives/CE9MS66BS/p1764062775876329

Aside from that, includes some formatting in the modules.config files (you can just ignore most of the changes there). I also added the missing meta.yml for binning_metabinner and fixed the components of other meta files.

NOTE: qsv/cat module uses topics, so I removed the explicit mixing into the versions channel.

Closes #871

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
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  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
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  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
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@dialvarezs dialvarezs changed the title Fix busc report concat Fix BUSCO and TIARA report concatenation Nov 27, 2025
@dialvarezs dialvarezs linked an issue Nov 27, 2025 that may be closed by this pull request
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@jfy133 jfy133 left a comment

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Not tested, but I don't see anything obvious

Comment thread CHANGELOG.md
@dialvarezs dialvarezs merged commit 877848f into nf-core:dev Nov 28, 2025
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CSVTK can cause pipeline fail when BUSCO output has uneven columns

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