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Commits on Dec 8, 2025

• semibin/singleeasybin: bump version + migrate to topics (#9517)

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  dialvarezs

  and

  mashehu

  authored
  180c9a9

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• Update haplogrep3 recipe to use topics (#9523)

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  ramprasadn

  and

  nf-core-bot

  authored
  c95c605

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• qsv/cat: bump version (#9518)

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  dialvarezs

  authored
  e7cb586

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• 🔧 update image and bioconda container for VueGen to latest version (#9201)

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  3 peopleauthored
  ef832d0

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• chore(deps): update infrastructural dependencies

  renovate[bot]

  authored
  21c7f09

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Commits on Dec 7, 2025

• Add strdrop/build (#9512)

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  fellen31

  authored
  aa1859b

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• fix(decoupler): reorder imports and ensure environment variables are … (#9516)

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  atrigila

  authored
  a5aa81b

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Commits on Dec 5, 2025

• fix(anota2seq): add gene IDs and handle empty results (#9510)

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  pinin4fjords

  and

  suhrig

  authored
  6717b61

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• anota2seq: wrong variable name for batch assignment (#9511)

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  suhrig

  authored
  c93d7d1

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• fix sambamba depth stub version (#9509)

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  fellen31

  authored
  ca6da11

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• update and add topics to snakemake module (#9454)

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  maxulysse

  and

  mashehu

  authored
  4613fce

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Commits on Dec 4, 2025

• meta.yml schema: add `containers` section, fix order and simplify (#9503)

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  mashehu

  authored
  25e0cf8

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• Update test files for Glimpse (#9467)

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  3 peopleauthored
  d911d93

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Commits on Dec 3, 2025

• fix fasta_index_methylseq and fastq_align_dedup workflows (#9496)

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  sateeshperi

  authored
  654daca

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• Sambamba depth add region bed input (#9498)

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  peterpru

  and

  fellen31

  authored
  b093f74

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• tcoffee_extractfrompdb test: sort file listing so "first" file is deterministic (#9489)

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  nathanweeks

  and

  mashehu

  authored
  9f00432

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• add new ontology term to tcoffee align (#9497)

  mirpedrol

  authored
  e3da0d1

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Commits on Dec 2, 2025

• Update semibin/singleeasybin environment (#9495)

  dialvarezs

  authored
  70e28be

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• Update shinyngs modules to latest release (#9488)

  delfiterradas

  authored
  33cc5a3

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• Fix hisat2/align to support large genome indices (.ht2l) (#9493)

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  pinin4fjords

  and

  claude

  authored
  5ec0e05

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• utils_nfcore_pipeline: fix small lang server error (#9492)

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  matthdsm

  authored
  df4d1c8

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• Declare deepvariant optional html output (#9469)

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  peterpru

  and

  ramprasadn

  authored
  bb9a292

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Commits on Dec 1, 2025

• Enable complex contrast strings in DESeq2 (#9473)

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  delfiterradas

  authored
  d09b58a

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• Add module PBMARKDUP (#9457)

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  sainsachiko

  authored
  c984ada

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• Add ontologies to tcoffee/regressive and upp/align modules (#9484)

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  mirpedrol

  authored
  c17afe7

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• chore(deps): update dependency prettier to v3.7.3 (#9483)

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  renovate[bot]

  authored
  4b9b410

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• chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 (#9480)

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  renovate[bot]

  authored
  96148e5

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• chore(deps): update infrastructural dependencies

  renovate[bot]

  authored
  cd7c390

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Commits on Nov 29, 2025

• fix(ribodetector): Add version snapshot for topic-based version collection (#9478)

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  pinin4fjords

  and

  claude

  authored
  43c983c

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• feat(fastq_qc_trim_filter_setstrandedness): Add Bowtie2 as alternative rRNA removal tool (#9474)

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  pinin4fjords

  and

  claude

  authored
  61ce58a

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Commits on Nov 28, 2025

• Merge modules with new topics syntax (#9333)

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  11 peopleauthored
  0b24358

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• 9396 new subworkflow fastq decontaminate deacon hostile (#9441)

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  Baksic-Ivan

  and

  vagkaratzas

  authored
  f3fb87a

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Commits on Nov 27, 2025

• feat(fastq_qc_trim_filter_setstrandedness): Add RiboDetector as alternative rRNA removal tool (#9462)

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  3 peopleauthored
  99590bc

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• qsv/cat: add option to skip input format checking (#9472)

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  dialvarezs

  authored
  dff559d

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• patch version update (#9471)

  vagkaratzas

  authored
  0d75d9a

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