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Commits on Aug 22, 2025

• METAPHLAN_METAPHLAN: update to support optional SAM output (#8937)

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  jfy133

  and

  SPPearce

  authored
  45b4cc6

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• Adds seq2hla (#8939)

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  FriederikeHanssen

  authored
  dfa786c

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• Update memory to return int (#8938)

  mahesh-panchal

  authored
  3351c21

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Commits on Aug 21, 2025

• update ensemblvep from 113.4 to 114.2 - and remove download from all annotation tests by using s3://annotation-cache (#8936)

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  maxulysse

  and

  mirpedrol

  authored
  48ca3de

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• New module: taxonkit/list (#8680)

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  jcbioinformatics

  and

  famosab

  authored
  c7f8619

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• lint + code polish sentieon (#8923)

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  maxulysse

  and

  nf-core-bot

  authored
  2565571

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• Update actions/setup-java action to v5

  renovate[bot]

  authored
  49bd07c

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• properly add secrets (#8934)

  maxulysse

  authored
  e18fe77

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• Add new subworkflow: tiff_segmentation_vpt (#8849)

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  mcmero

  and

  prototaxites

  authored
  6533d29

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Commits on Aug 20, 2025

• Fix optional output in starfusion/detect (#8933)

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  nvnieuwk

  authored
  b0f38d0

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• add secrets (#8932)

  maxulysse

  authored
  d3648cd

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• [prettier] (#8930)

  muffato

  authored
  40ab92f

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• Update update-sentieon-snapshot.yml (#8929)

  maxulysse

  authored
  a5b14d6

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• add .github/workflows/update-sentieon-snapshot.yml GHA (#8928)

  maxulysse

  authored
  91cbfc3

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• Delete .editorconfig (#8918)

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  maxulysse

  authored
  2f35bad

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• lint + code polish ngscheckmate/ncm (#8922)

  maxulysse

  authored
  5e3fd0c

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• lint + code polish lofreq/callparallel (#8921)

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  maxulysse

  authored
  8c0cf19

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• lint + code polish goleft/indexcov (#8920)

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  maxulysse

  authored
  2f95538

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• lint + code polish fgbio/fastqtobam (#8919)

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  maxulysse

  authored
  16af457

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• lint + code polish bcftools/annotate (#8916)

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  maxulysse

  authored
  8b09455

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• lint + code polish ascat (#8915)

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  maxulysse

  authored
  e88b4e5

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Commits on Aug 19, 2025

• Update CODEOWNERS (#8909)

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  maxulysse

  and

  SPPearce

  authored
  1b6f41a

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• update applybqsr modules and tests (#8914)

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  maxulysse

  authored
  c707c63

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• BUSCO 6 update (#8781)

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  3 peopleauthored
  de5b678

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• New module: sigprofiler (#8698)

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  kdavydzenka

  and

  LouisLeNezet

  authored
  71ca1bd

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Commits on Aug 18, 2025

• Fix YaHS bug (#8913)

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  prototaxites

  authored
  2710e8f

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• add writing index option to samtools sort (#8895)

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  ljwharbers

  and

  nf-core-bot

  authored
  e89ff68

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• lint | format | fix | polish on all gatk4 (#8901)

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  maxulysse

  authored
  a572532

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• Update vcflib to language server (#8912)

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  famosab

  and

  maxulysse

  authored
  401ec2b

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• split out from #8901 (#8905)

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  maxulysse

  authored
  e25f4fa

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• index should be emitted as either tbi or csi (#7385)

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  4 peopleauthored
  dd78204

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Commits on Aug 16, 2025

• chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.12.9 (#8903)

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  renovate[bot]

  authored
  be2d36a

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• Add coverm/genome (#8874)

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  3 peopleauthored
  7cc7dd5

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Commits on Aug 15, 2025

• Update CODEOWNERS (#8907)

  maxulysse

  authored
  d744543

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• Fixing pre-commit (#8902)

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  maxulysse

  authored
  e7bf771

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