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Commits on Oct 27, 2025

• Update bases2fastq (#9253)

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  SPPearce

  authored
  01bfb37

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• Add samtools/splitheader and deprecate samtools/getrg (#9250)

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  prototaxites

  authored
  96b96cd

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• bump multiqc to 3.12 🖤 (#9251)

  mashehu

  authored
  af27af1

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• adding new module gatk4_concordance (#9247)

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  kubranarci

  and

  SPPearce

  authored
  98c35fb

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• Removed stray " (#9248)

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  FernandoDuarteF

  authored
  7a72607

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Commits on Oct 26, 2025

• Pin python version in conda environment for GTDBTK modules to match containers (#9249)

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  jfy133

  and

  SPPearce

  authored
  5e433c4

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Commits on Oct 25, 2025

• Update actions/upload-artifact action to v5

  renovate[bot]

  authored
  a4605bf

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Commits on Oct 24, 2025

• update module pbjasmine meta.yml structure (#9235)

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  YiJin-Xiong

  authored
  5e00a5b

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• Update module modkit metayml (#9237)

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  YiJin-Xiong

  authored
  f274c18

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• update module fibertoolsrs meta.yml structure (#9236)

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  YiJin-Xiong

  authored
  b29fd98

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Commits on Oct 23, 2025

• Update EIDO module (#9216)

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  khoroshevskyi

  authored
  707ead6

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• Bump TRGT to 4.0.0 (#9234)

  fellen31

  authored
  90b580b

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• Bump Severus to 1.6 (#9233)

  fellen31

  authored
  98a699d

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• Add export BLASTDB to blastn module (#9227)

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  AnnaNoren

  authored
  d46ce18

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• Bump Sawfish to 2.2.0 (#9232)

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  fellen31

  authored
  08d6e3c

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• change to stageinmode copy for fq2bam (#9229)

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  famosab

  authored
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Commits on Oct 22, 2025

• Support uncompressed files too in seqkit/split2 (#9228)

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  muffato

  authored
  55a02f5

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• fixed channel order in feryja (#9226)

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  svarona

  authored
  e843854

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• Update BAKTA/BAKTA version and add missing input file channels (#9223)

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  jfy133

  and

  SPPearce

  authored
  72c9835

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• Adding cnaqc tool module (#8890)

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  vvvirgy

  and

  famosab

  authored
  a124b81

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• Bump longphase/haplotag to 2.0 (#9225)

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  fellen31

  authored
  155db46

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• Add GATK4 to the PureCN container image and to Conda requirements (#9217)

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  lbeltrame

  authored
  17dc773

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Commits on Oct 21, 2025

• update module dysgu to dysgu/run (#9220)

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  nvnieuwk

  and

  mashehu

  authored
  d64e7ce

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• fix fq2bam symlinks (#9219)

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  famosab

  authored
  8bce257

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• Add diann subworkflow and module (#9173)

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  pinin4fjords

  and

  claude

  authored
  310549b

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• Fq2bam new (#9212)

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  famosab

  and

  gburnett-nvidia

  authored
  d41a0be

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• Fastcov updates (#9213)

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  5 peopleauthored
  2589c8a

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Commits on Oct 20, 2025

• Update showinf to clean outputs (#9214)

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  AlexBarbera

  authored
  65a4ca6

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• Collect the most accurate alignment statistic. (#9210)

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  charles-plessy

  authored
  970f05b

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Commits on Oct 18, 2025

• Update GitHub Actions

  renovate[bot]

  authored
  d872163

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• Update GitHub Actions

  renovate[bot]

  authored
  bc0f16a

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Commits on Oct 17, 2025

• Fix bug #9203: Downstream operations fail because cellranger mkfastq doesn't split index and primary FASTQ files (#9204)

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  3 peopleauthored
  eede6ba

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• fix linting for mosdepth and umitools/extract (#9207)

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  maxulysse

  authored
  d855e94

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• Update/portcullis/full (#9187)

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  3 peopleauthored
  92c8ece

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• Update meta.yml (#9060)

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  lucacozzuto

  authored
  ecf739d

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