All pull requests

Pull requests

• Update bwameth to 0.2.10

  size/xl
  #13486·heuermh opened Oct 28, 2026Contributor·17 tasks·

  ·
  1

• utils_nfcore_pipeline: keep trailing zeros in software versions

  size/s
  #13483·bhargavchintam opened Oct 28, 2026·4 of 6 tasks·

  ·
  3

• new module: insitugame

  size/m
  #13471·Lukecele opened Oct 27, 2026Contributor·6 of 7 tasks·

  ·
  14

• fix typo

  size/s
  #13469·bounlu opened Oct 27, 2026Contributor·

  ·
  1

• docs: fix dead link to the module contribution guide in README

  size/xs
  #13467·filipetessaro opened Oct 26, 2026·1 task done·

  ·
  1

  1

• utils_nextflow_pipeline: fix crash in checkCondaChannels when conda is not on PATH

  size/xs
  #13466·filipetessaro opened Oct 26, 2026·2 of 4 tasks·

  ·
  1

  1

• Add scdblfinder module

  size/xl
  #13465·iraajgangavaram opened Oct 26, 2026·17 tasks·

  ·
  27

• gatk4/haplotypecaller: emit realigned BAM index

  size/s
  #13460·asp8200 opened Oct 26, 2026Contributor·

  ·
  1

• scvitools/solo: retain the SCVI model across batches

  size/s
  #13451·nictru opened Oct 25, 2026Contributor·6 tasks done·

  ·

• fix(labeller): skip conda-lock files for PR size labelling

  size/xl
  #13446·prototaxites opened Oct 23, 2026Contributor·17 tasks·

  ·
  2

• parabricks/mutectcaller: pass --pon to mutectcaller

  size/l
  #13440·FriederikeHanssen opened Oct 22, 2026Contributor·9 of 14 tasks·

  ·

• new module: celltypist

  size/xl
  #13438·iraajgangavaram opened Oct 22, 2026·11 of 14 tasks·

  ·
  30

• Create mtx2h5ad module

  size/xl
  #13427·delfiterradas opened Oct 20, 2026Contributor·17 tasks·

  ·
  1

  3

• New module: onkopus/run

  size/xl
  #13387·vagkaratzas opened Oct 18, 2026Contributor·11 of 14 tasks·

  ·
  1

  38

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

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

  ·

• Update blast to seqera containers

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

  ·
  1

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

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

  ·
  1

  4

• Merge BAM_SOMATIC_VARIANT_CALLING_GATK subworkflows

  size/l
  #13335·beatrizsavinhas opened Oct 16, 2026Contributor·4 of 17 tasks·

  ·
  33

  

• Update gridss to use Seqera Containers

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

  ·
  1

  1

• plink/homozyg module

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

  ·
  2

• New module: metabinner/gencoveragefile

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

  ·
  1

  61

  

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

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

  ·
  1

  10

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

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

  ·
  3

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

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

  ·
  11

• New module: plink2/makepgen

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

  ·
  5