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Commits on Sep 8, 2025

• Update msisensor2/scan and msisensor2/msi (#9005)

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  maxulysse

  and

  SPPearce

  authored
  3dd258a

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• Add --columns-file argument to bcftools annotate (#9000)

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  heuermh

  authored
  28438d3

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Commits on Sep 7, 2025

• 8705 picardcollecthsmetrics fails for gzipped genomes (#8974)

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  shivangi-7

  authored
  bd597f1

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Commits on Sep 5, 2025

• Update module: sparsesignatures (#8950)

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  kdavydzenka

  and

  SPPearce

  authored
  1b59fef

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• chore(deps): update actions/github-script action to v8

  renovate[bot]

  authored
  d935734

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Commits on Sep 4, 2025

• chore(deps): update github actions

  renovate[bot]

  authored
  36c0e97

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• update toulligqc to 2.7.1 and fix plotly dependency in -profile conda (#8997)

  Daniel-VM

  authored
  f1ac3c7

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• Bump/ensembl vep (#8995)

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  matthdsm

  authored
  2fcc537

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• Update BWAMEM2_INDEX (#8993)

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  3 peopleauthored
  b290204

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• Update main.nf (#8985)

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  lucacozzuto

  authored
  0a5bbb6

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• Fix abra2 versions snapshot (#8994)

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  maxulysse

  authored
  2d15090

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Commits on Sep 3, 2025

• module: Abra2 for INDEL realignment (#8986)

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  adamrtalbot

  authored
  c83abe8

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• Update RGI modules to 6.0.5 (#8989)

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  jfy133

  and

  SPPearce

  authored
  531d8a4

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Commits on Sep 2, 2025

• fix(glnexus): output channel is no longer optional (#8982)

  awgymer

  authored
  9b696bd

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• Fix GLNexus: remove optional VCF output and update tests (#8981)

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  awgymer

  authored
  3b71cef

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Commits on Sep 1, 2025

• New module: modkit/bedmethyltobigwig (#8965)

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  Schmytzi

  authored
  6a12858

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• Sbwf migrate rnafusion (#8972)

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  atrigila

  and

  nvnieuwk

  authored
  5ce6cef

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• removed empty folder (#8977)

  vagkaratzas

  authored
  f8c29d8

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• new moduke: seqkit/sana (#8975)

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  vagkaratzas

  and

  nvnieuwk

  authored
  1f3c713

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• bump vcfanno to 0.3.7 (#8976)

  nvnieuwk

  authored
  15e7f21

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Commits on Aug 29, 2025

• Add id to tag (#8970)

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  SusiJo

  authored
  48ea3c4

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• Update nanoplot to 1.46.1 (#8968)

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  Daniel-VM

  authored
  9322f99

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• Bump artic_aligntrim version (#8969)

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  BioWilko

  authored
  da115c2

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Commits on Aug 28, 2025

• New module: Slamdunk/All (#8955)

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  HaidYi

  authored
  65725f3

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• feat: support no reference tumor only cnvkit analysis (#8618)

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  znorgaard

  authored
  09223d6

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• Update DIAMOND_*: Update all DIAMOND modules to satisfy Nextflow language server (#8966)

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  3 peopleauthored
  c44e4bb

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• Add another csv file as output (#8878)

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  LuisHeinzlmeier

  authored
  0cb9946

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Commits on Aug 27, 2025

• Bump dupRadar version (#8925)

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  edmundmiller

  authored
  2b7952f

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• Update blastn module (#8765)

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  3 peopleauthored
  4545045

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• Fix version in snapaligner/index stub (#8961)

  SPPearce

  authored
  8040783

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• small push (#8960)

  vagkaratzas

  authored
  85f5983

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• Add artic/aligntrim module (#8943)

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  3 peopleauthored
  3fa028f

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• Subworkflow mmseqs fasta cluster (#8952)

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  vagkaratzas

  and

  Joon-Klaps

  authored
  987da3b

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• use prefix and suffix for applybqsr (gatk4 + gatk4spark) (#8947)

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  maxulysse

  and

  SPPearce

  authored
  620300d

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• Update samtools merge tests (#8953)

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  SPPearce

  authored
  7d5646d

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