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Commits on Aug 8, 2025

• Adding mem2 switch to fasta_index_bismark_bwameth subworkflow (#8867)

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  mbeavitt

  authored
  8777e22

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• Migrate `STARFUSION_DETECT` local module (#8813)

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  delfiterradas

  and

  atrigila

  authored
  310a7a5

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• Update samtools mpileup meta (#8865)

  SPPearce

  authored
  0fcfdcd

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• chore(deps): update actions/cache digest to 0400d5f

  renovate[bot]

  authored
  54d5c32

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Commits on Aug 7, 2025

• Bff (#8653)

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  LuisHeinzlmeier

  and

  nictru

  authored
  ab0581e

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• Add stub for vsearch/cluster (#8860)

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  famosab

  authored
  3bc4793

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• update krakentools version 1.2.1 (#8858)

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  MarieLataretu

  authored
  9f58e4d

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• update module: PERBASE (#8854)

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  camlloyd

  authored
  9af058a

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• feat: Add fastplong module (#8857)

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  Lupphes

  authored
  88869fc

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Commits on Aug 6, 2025

• Fix some modules related to the hadge pipeline (#8767)

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  nictru

  and

  LuisHeinzlmeier

  authored
  6d8e4eb

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Commits on Aug 4, 2025

• Adding bwa-mem2 mode test to bwameth/align (#8846)

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  mbeavitt

  authored
  a9807fa

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• Update bismark to 0.25 (#8845)

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  SPPearce

  authored
  8784324

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Commits on Aug 3, 2025

• Adding mem2 mode to bwameth/index (#8838)

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  3 peopleauthored
  6969ca9

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Commits on Aug 2, 2025

• Improve scrublet batch_col handling (#8843)

  nictru

  authored
  57325b5

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Commits on Aug 1, 2025

• Update `rrnatranscripts` and add new module `agat/convertgff2bed` (#8842)

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  atrigila

  and

  rannick

  authored
  b785bb0

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• Add scanpy/pca module (#8702)

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  nictru

  authored
  f4430fa

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• Update oras to https (#8724)

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  5 peopleauthored
  71e0a05

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• feat: Add trimal module (#8826)

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  IceGreb

  and

  vagkaratzas

  authored
  a5e2319

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Commits on Jul 31, 2025

• add ctatsplicing/prepgenomelib and ctatsplicing/startocancerintrons (#8144)

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  anoronh4

  and

  delfiterradas

  authored
  8476d6a

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• Move YaHS inputs to single tuple (#8833)

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  prototaxites

  authored
  f23a6c5

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Commits on Jul 30, 2025

• update kma/index to v1.5.0 and change to seqera containers (#8834)

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  HaidYi

  authored
  90bb6d2

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• New module: KMA (based on https://github.com/nf-core/modules/pull/7251) (#8718)

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  HaidYi

  and

  famosab

  authored
  5138a66

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• Add new module varscan/fpfilter (#8812)

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  vmelichar

  and

  famosab

  authored
  ff79ec0

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• Fix meta of fastqutils/info and update version to 0.25.3 (#8832)

  famosab

  authored
  bf5f37e

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• New module: vizgenpostprocessing/compiletilesegmentation (#8803)

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  mcmero

  and

  famosab

  authored
  cf734b9

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Commits on Jul 29, 2025

• clipkit keywords (#8830)

  vagkaratzas

  authored
  5a0f7c1

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• add new module: deeptools/multibigwigsummary (#8824)

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  ugoiannacchero

  and

  SPPearce

  authored
  6be688f

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• Add some keywords to copyumifromreadname (#8828)

  SPPearce

  authored
  47dbfc0

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• Remove defaults channel from cooltools/insulation (#8827)

  SPPearce

  authored
  23272c1

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• Update keywords from default (#8829)

  fellen31

  authored
  b679e54

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• New module: comebin/runcomebin (#8825)

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  prototaxites

  authored
  b153ee5

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• New module: vamb/bin (#8816)

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  prototaxites

  and

  jfy133

  authored
  27e3168

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• `last/maf-convert`: stop exporting `fasta` when converting to `cram`. (#8822)

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  charles-plessy

  authored
  c1de1f6

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Commits on Jul 28, 2025

• update PDB ontology (#8819)

  mirpedrol

  authored
  7fb8d8f

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• Run pre-commit on meta and env files for varlociraptor (#8815)

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  famosab

  authored
  3179219

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