All pull requests

Pull requests

• easypqp/convert, easypqp/library: bump to 0.1.60

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  #13374·jonasscheid opened Oct 17, 2026Contributor·4 of 6 tasks·

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• Update tcoffee to use Seqera Containers

  size/xl
  #13373·mribeirodantas opened Oct 17, 2026Member·

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  1

  1

• Update taxonkit to use Seqera Containers

  size/l
  #13371·mribeirodantas opened Oct 17, 2026Member·

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  1

• fix(cellranger/multi): preserve R1 tokens in sample names

  size/xs
  #13369·Sriiraam opened Oct 16, 2026·5 of 6 tasks·

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• feat(panteraga): add panteraga module

  size/xl
  #13366·prototaxites opened Oct 16, 2026Contributor·17 tasks·

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  1

• viennarna: Update to use Seqera containers

  size/xl
  #13353·renatosantos98 opened Oct 16, 2026Member·

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  1

  1

• Update blast to seqera containers

  size/xl
  #13344·Tabea01 opened Oct 16, 2026Contributor·

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• snpeff/snpeff: add optional canonList input (paired run #2)

  size/s
  #13339·HR-cruk opened Oct 16, 2026Contributor·11 of 15 tasks·

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  4

• Merge BAM_SOMATIC_VARIANT_CALLING_GATK subworkflows

  size/l
  #13335·beatrizsavinhas opened Oct 16, 2026Contributor·17 tasks·

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• New module: vardictrust (VarDictRust variant caller)

  size/xl
  #13322·palakpsheth opened Oct 16, 2026·13 of 14 tasks·

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  6

• star/genomegenerate: leave 10% of task memory as headroom for STAR

  size/xs
  #13292·danilomonge opened Oct 16, 2026·2 of 3 tasks·

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  1

• Update quilt to use Seqera Containers

  size/xl
  #13270·mribeirodantas opened Oct 16, 2026Member·

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• Update gridss to use Seqera Containers

  size/xl
  #13266·mribeirodantas opened Oct 16, 2026Member·

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• plink/homozyg module

  size/l
  #13254·Othmanaljurayyad opened Oct 15, 2026·

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• New module: metabinner/gencoveragefile

  size/xl
  #13214·HR-cruk opened Oct 15, 2026Contributor·11 of 14 tasks·

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  43

  

• Update vt to use Seqera Containers and bump to version 0.57721

  size/xl
  #13212·renatosantos98 opened Oct 15, 2026Member·

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• snpeff/snpeff: add optional canon_list input (-canonList)

  size/m
  #13193·siddharthjayaraman opened Oct 15, 2026Member·11 of 17 tasks·

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• samtools/flagstat,idxstats: convert to static record types

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  #13176·luisas opened Oct 15, 2026Contributor·2 tasks·

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  3

• interproscan: strip '*' from protein sequences

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  #13160·danilodileo opened Oct 15, 2026Contributor·4 tasks done·

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• New module: infernal cmscan

  size/m
  #13150·sainsachiko opened Oct 14, 2026Contributor·14 of 17 tasks·

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  16

• varnet: bump to 1.5.4, version from --version, tumor-only support

  size/m
  #13147·kiranchari opened Oct 14, 2026Contributor·17 tasks·

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  4

• New module: plink2/makepgen

  size/m
  #13145·malghuraybi opened Oct 13, 2026·12 of 14 tasks·

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• mirdeep2/mirdeep2, mirdeep2/mapper: use process_single

  size/xs
  #13131·OtoYuki opened Oct 12, 2026·2 tasks done·

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  1

• Trident validate

  size/m
  #13128·TCLamnidis opened Oct 12, 2026Contributor·10 of 17 tasks·

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  3

• PROOF OF CONCEPT: samtools/multicommand - #11550

  size/xl
  #13127·prototaxites opened Oct 12, 2026Contributor·17 tasks·

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  2