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Commits on Nov 19, 2025

• Hificnv—copy-number variant caller for PacBio HiFi long-read data (#9165)

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  chaochaowong

  and

  inemesb

  authored
  0cf688b

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• Update geNomad modules (#9413)

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  dialvarezs

  authored
  775256e

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Commits on Nov 18, 2025

• run pre-commit rules on all files (#9416)

  mashehu

  authored
  e753770

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• Backsub update - 0.5.1 (#9422)

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  kbestak

  authored
  00a810c

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• New module: sambamba/depth (#9393)

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  peterpru

  authored
  dd10345

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• Update to cellranger update v10.0.0 (#9417)

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  3 peopleauthored
  a772a68

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• fix: Add stub files to MultiQC empty directories for AWS Batch/S3 compatibility (#9419)

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  SZhengP

  authored
  82a7918

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Commits on Nov 17, 2025

• Add genetic map to `STITCH` module (#9408)

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  LouisLeNezet

  and

  LouisLeNezet

  authored
  7fb11b3

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• truvari/bench update: output log.txt (#9415)

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  kubranarci

  authored
  94c8a56

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• update topics structure in meta.yml (#9412)

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  mirpedrol

  and

  mashehu

  authored
  88cf2e2

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• Fix issues in chromograph module (#9395)

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  fellen31

  authored
  c23ac76

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• Add stub tests to kraken2/kraken2 nf-core module (#9289)

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  3 peopleauthored
  1a9dc0f

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Commits on Nov 14, 2025

• Deprecating custom_getchromsizes (#9367)

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  apetizerr

  and

  SPPearce

  authored
  bd1b6a4

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• Swap tabix to only one output channel (#9346)

  SPPearce

  authored
  61846a0

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• Change varlociraptor inputs to one channel and update (#9404)

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  famosab

  authored
  5ef2a21

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• Fix sample name mangling in tximport (#9407)

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  pinin4fjords

  authored
  d205ebc

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• Add methbat/profile module (#9385)

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  inemesb

  authored
  0d6c083

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• add eval as channel type (#9405)

  mashehu

  authored
  daa7e49

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Commits on Nov 13, 2025

• Updates for souporcell (#9363)

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  LuisHeinzlmeier

  and

  nictru

  authored
  6998ba9

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• bbmap/bbsplit: Fix newline at end of file in meta.yml (#9399)

  pinin4fjords

  authored
  fa14771

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• Syntax updates to the picard modules (#9398)

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  nvnieuwk

  authored
  4e84154

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• Repair all modules not declaring `conda environment.yml` in `main.nf (#9397)

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  jfy133

  and

  SPPearce

  authored
  c16667b

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Commits on Nov 12, 2025

• Syntax update for wisecondorx/newref (#9394)

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  nvnieuwk

  authored
  5bee37f

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• Add SYLPH/SKETCHGENOMES (#9392)

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  3 peopleauthored
  b8a54d9

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• Fix channel method call in softwareVersionsToYAML (#9375)

  nvnieuwk

  authored
  271e7fc

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• Fix syntax issues in somalier modules (#9378)

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  nvnieuwk

  authored
  fdb27ae

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• Update SYLPH to 0.9.0, fix SYLPH/SKETCH meta.yaml, and make SYLPH/SKETCHSAMPLES (#9389)

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  jfy133

  and

  SPPearce

  authored
  bd80e43

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• Update dependency nextflow-io/nextflow to v24.10.9 (#9391)

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  renovate[bot]

  authored
  5affa1b

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• Update pre-commit hook python-jsonschema/check-jsonschema to v0.35.0 (#9390)

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  renovate[bot]

  authored
  121f431

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• Update all DIAMOND versions to latest version (#9387)

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  jfy133

  and

  SPPearce

  authored
  4012b87

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Commits on Nov 11, 2025

• picrust2/pipeline: correcting keys in meta.yml (#9386)

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  mashehu

  authored
  2c57693

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• Update blastn meta.yml (#9384)

  d4straub

  authored
  9da6f5c

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• Allow non-count data in DREAM (#9254)

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  delfiterradas

  and

  atrigila

  authored
  0173f3c

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• Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.4 (#9317)

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  renovate[bot]

  authored
  8f2120a

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• Update dependency seqeralabs/wave-cli to v1.7.0 (#9383)

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  renovate[bot]

  authored
  68aa4d8

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