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Commits on Oct 8, 2025

• Add Pypolca module (#9176)

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  dwells-eit

  and

  Joon-Klaps

  authored
  dd01970

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Commits on Oct 7, 2025

• Gzi input for mutect2 (#9043)

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  3 peopleauthored
  3e3ffe7

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Commits on Oct 6, 2025

• Add slamdunk/map module (#8967)

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  HaidYi

  and

  famosab

  authored
  3b23d78

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• Add validation of meta.yml keywords (#9174)

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  mirpedrol

  authored
  fe9d645

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Commits on Oct 4, 2025

• Update all hAMRonization modules to latest version (#9171)

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  jfy133

  and

  SPPearce

  authored
  9b7b083

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• Update amrfinderplus modules to latest version (#9170)

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  jfy133

  and

  SPPearce

  authored
  a621003

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Commits on Oct 3, 2025

• Updated BLAST modules (#9168)

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  GallVp

  authored
  6330227

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Commits on Oct 2, 2025

• Make SAMTOOLS_COVERAGE fasta ref input / index optional (#9166)

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  BioWilko

  authored
  c3ca2a1

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• Change KRAKEN_ADD module emission and KRAKEN_BUILD input to fix symlink-inside-symlink container incompatibilty (#9163)

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  jfy133

  and

  JoseEspinosa

  authored
  dc32c68

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Commits on Oct 1, 2025

• New fasta index (#9067)

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  5 peopleauthored
  0f763f1

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• update varlociraptor (#9162)

  famosab

  authored
  78cc4e9

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Commits on Sep 30, 2025

• Rastair fix (#9158)

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  3 peopleauthored
  a4f1768

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• new subworkflow: fasta_vclust_prefilter_align_cluster (#9157)

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  Joon-Klaps

  authored
  e809236

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Commits on Sep 29, 2025

• Sort inputs to sawfish joint-call to create reproducible outputs (#9154)

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  fellen31

  authored
  7177f83

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• fix: nf-test in strelka (#8241)

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  famosab

  and

  SPPearce

  authored
  039730f

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• Add cramino module (#9145)

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  inemesb

  authored
  b4a9c21

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• vep: fix recipe build (#9153)

  matthdsm

  authored
  0567eee

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• new module: modkit/repair (#9077)

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  3 peopleauthored
  b5584db

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Commits on Sep 26, 2025

• Bump basicpy container revision (#9142)

  jmuhlich

  authored
  42d6134

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• filter differential genes now outputs up and down regulated genes as well (#9094)

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  akaviaLab

  authored
  aeccbde

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• Fixing bismark stubs and updating tests (#9008)

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  3 peopleauthored
  107a3fb

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• Add module ngsbits updhunter (#9146)

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  matthdsm

  and

  vagkaratzas

  authored
  ae8668d

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• Add module csvtk/sort (#9147)

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  LeonHafner

  authored
  d01263b

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• Bump version Kraken2 to 2.1.6 (#9139)

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  DLBPointon

  authored
  0821737

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• new module: fibertools-rs (#9102)

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  YiJin-Xiong

  authored
  41bb4c9

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• version bump, added stub test (#9143)

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  vagkaratzas

  authored
  5c07517

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• Update deeptools modules: bamcoverage, multibamsummary, multibigwigsummary (#9129)

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  nadiaxaidan

  and

  SPPearce

  authored
  bef1bd6

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• New nf-core subworkflow - faa seqfu seqkit (#9136)

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  vagkaratzas

  authored
  15c0a79

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Commits on Sep 25, 2025

• MuSE: change to htslib for bgzip and tabix & language server (#9137)

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  famosab

  authored
  e3933b2

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• Parabricks STAR (and stargenomegenerate old version for compatibility) (#9062)

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  3 peopleauthored
  fe77c64

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• add pbtk/pbmerge module (#9127)

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  HaidYi

  and

  famosab

  authored
  8c62f14

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• Update wipertools/fastqgather (#8931)

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  4 peopleauthored
  64f84f5

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• fix(metaeuk/easypredict): add threads argument to command (#9135)

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  prototaxites

  authored
  47aa188

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• bump ensemblvep (again) (#9134)

  matthdsm

  authored
  b6d0f77

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• chore(deps): update actions/cache digest to 0057852

  renovate[bot]

  authored
  94f9d67

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