All pull requests

Pull requests

• New module: cnvkit/referencepooled (pooled-normal reference)

  #13074·barlowa124 opened Oct 1, 2026·12 of 14 tasks·

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  1

• fastq_qc_trim_filter_setstrandedness: add opt-in failure on undetermined strandedness

  Ready for Review
  #13073·pinin4fjords opened Oct 1, 2026Member·

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• add t2pmhc modules (graph creation and prediction)

  #13072·mapo9 opened Oct 1, 2026Contributor·12 tasks done·

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  1

• feat: huggingface/download: support whole repository downloads

  Ready for Review
  #13071·mwiewior opened Oct 1, 2026Contributor·13 tasks done·

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  1

• feat: Add vcf_annotate_vepyr subworkflow

  #13070·mwiewior opened Oct 1, 2026Contributor·12 of 14 tasks·

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• Update spades to 4.3.0

  #13068·barlowa124 opened Oct 1, 2026·9 of 14 tasks·

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  1

• cellranger/multi: add V(D)J chain-type inputs (VDJ-T, VDJ-T-GD, VDJ-B)

  draft
  #13067·nathanweeks opened Sep 30, 2026Member·9 of 11 tasks·

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  1

• feat: add colabfold module

  #13066·Bboy010 opened Sep 30, 2026·5 tasks done·

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• feat: add tmalign module

  #13065·Bboy010 opened Sep 30, 2026·14 tasks done·

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• Update deseq2/differential to support apeglm shrinkage

  size/xl
  #13061·priyalT opened Sep 30, 2026·3 of 6 tasks·

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  6

• parabricks/fq2bam - Add known sites tbi

  #13056·famosab opened Sep 29, 2026Contributor·17 tasks·

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  1

• bcftools/query: move ext.suffix to an input

  #13037·Totejolo opened Sep 25, 2026·9 of 12 tasks·

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• ENH: provided fix for issue 13034

  #13036·Melclic opened Sep 25, 2026·10 of 17 tasks·

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• Add modkit/dmr module

  #13021·YannVRB opened Sep 23, 2026·11 of 13 tasks·

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  6

• Add new component: tantan

  Ready for Review
  #13017·snunzi opened Sep 23, 2026Contributor·12 tasks done·

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  6

• Update cellranger to version 10.1.0

  #13012·heuermh opened Sep 22, 2026Contributor·17 tasks·

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• 🔧 update to VueGen 0.7.0

  size/s
  #13010·enryH opened Sep 22, 2026Contributor·2 of 17 tasks·

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• Swap narfmap/hashtable to topics

  size/xl
  #13000·SPPearce opened Sep 19, 2026Contributor·

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  1

• Add custom/taxonomytree module and taxonomy2phylogeny subworkflow

  #12977·erikrikarddaniel opened Sep 16, 2026Member·13 of 17 tasks·

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  13

• freyja: update to 2.0.4

  #12964·pditommaso opened Sep 15, 2026Contributor·3 tasks done·

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  5

• Smudgeplot all

  size/m
  #12960·DLBPointon opened Sep 15, 2026Contributor·

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• metaproviz/internalstandard module #12957

  #12958·ChristinaSchmidt1 opened Sep 15, 2026·2 of 17 tasks·

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  16

• Update to topic universc

  #12955·LouisLeNezet opened Sep 14, 2026Contributor·17 tasks·

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  3

  

• Add crabs/merge module

  #12930·xHaMMaDy opened Sep 13, 2026Contributor·14 tasks done·

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• fix(manta): pin working biocontainer to avoid segfault

  #12929·kanishkanandhkumar opened Sep 11, 2026·1 of 2 tasks·

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