All pull requests

Pull requests

• unicycler - fix kmer_count default value

  #8921·RZ9082 opened Nov 13, 2026Member·2 of 8 tasks·

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• Updating tools/tesseract from version 5.5.3 to 5.5.4

  autobump
  #8920·gxydevbot opened Nov 13, 2026Collaborator·

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• Updating tools/semibin from version 2.5.0 to 2.6.0

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  #8919·gxydevbot opened Nov 13, 2026Collaborator·

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• Updating tools/perseus from version 1.2.0 to 1.3.0

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  #8918·gxydevbot opened Nov 13, 2026Collaborator·

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• Updating tools/checkm from version 1.2.5 to 1.3.0

  autobump
  #8917·gxydevbot opened Nov 13, 2026Collaborator·

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• varscan: update to 2.4.6

  #8916·bgruening opened Nov 12, 2026Member·

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  1

• beagle: update to 5.5

  #8915·bgruening opened Nov 12, 2026Member·

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  2

• Add SKESA

  BioHackEU26
  #8914·dannon opened Nov 12, 2026Member·9 of 13 tasks·

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  4

• Add mash triangle

  BioHackEU26skip-version-check
  #8913·dannon opened Nov 12, 2026Member·

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  7

• busco: pass --datasets_version for offline auto-lineage, fail clearly when the cached DB can't support it

  #8912·gkr0110 opened Nov 12, 2026Contributor·

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  5

• Ucsc chain tools

  ready-for-review
  #8910·richard-burhans opened Nov 12, 2026Member·5 of 8 tasks·

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  26

• Update tools/ragtag to 2.1.1

  paper-cutready-for-review
  #8908·SaimMomin12 opened Nov 12, 2026Contributor·3 of 8 tasks·

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• mags_visualization: update to 0.1.0, add overview_figure tool

  #8905·paulzierep opened Nov 11, 2026Contributor·4 of 5 tasks·

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• Mothur 1.48.6 upgrade

  skip-url-check
  #8904·bernt-matthias opened Nov 11, 2026Contributor·5 of 8 tasks·

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  4

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• Add COMEBin-LLMopt (faster COMEBin) wrapper

  #8903·paulzierep opened Nov 11, 2026Contributor·3 tasks done·

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• AleRax

  #8900·aparamitarana009-boop opened Nov 11, 2026Contributor·5 of 8 tasks·

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  38

• Update spatialdata

  #8894·nilchia opened Nov 10, 2026Collaborator·5 of 8 tasks·

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• query tabular: add quoted-outputs and more metadata for outputs

  #8887·bgruening opened Nov 8, 2026Member·

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  2

• Update tools/kleborate to 3.3.0b1

  ready-for-review
  #8844·SaimMomin12 opened Nov 2, 2026Contributor·5 of 8 tasks·

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  11

• Update mgnify_pipelines_toolkit suite

  ready-for-review
  #8843·RZ9082 opened Nov 2, 2026Member·4 of 8 tasks·

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  3

• seqfu suite (seqfu_check, seqfu_count, seqfu_stats)

  ready-for-review
  #8842·RZ9082 opened Nov 2, 2026Member·5 of 8 tasks·

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  15

• DADA2: consolidate binned-quality learning, histogram export and exact-species repair

  #8839·nekrut opened Oct 31, 2026Contributor·

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  7

• Kraken2: accept custom database files from history

  #8837·nekrut opened Oct 30, 2026Contributor·

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  7

• Add native SBDI submission and annotation exporters from AmpliSeq

  #8836·nekrut opened Oct 30, 2026Contributor·

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  1

  11

• Add native QIIME SIDLE wrappers for multiregion amplicon reconstruction

  #8831·nekrut opened Oct 30, 2026Contributor·

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  26