All pull requests

Pull requests

• perf: autobump geo/rasterio/clip/environment.yaml

  geo/rasterio/clip
  #5934·snakedeploy-bot[bot] opened Oct 9, 2026Bot·

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  1

• chore(master): release 9.19.1

  autorelease: pending
  #5928·snakemake-bot opened Oct 9, 2026Contributor·

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  1

• perf: autobump bio/orthanq/environment.yaml

  bio/orthanq
  #5888·snakedeploy-bot[bot] opened Sep 18, 2026Bot·

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  4

• perf: autobump bio/gatk/baserecalibratorspark/environment.yaml

  bio/gatk/baserecalibratorspark
  #5837·snakedeploy-bot[bot] opened Aug 28, 2026Bot·

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  1

• perf: autobump bio/gatk/markduplicatesspark/environment.yaml

  bio/gatk/markduplicatesspark
  #5836·snakedeploy-bot[bot] opened Aug 28, 2026Bot·

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  1

• perf: autobump bio/gatk/printreadsspark/environment.yaml

  bio/gatk/printreadsspark
  #5835·snakedeploy-bot[bot] opened Aug 28, 2026Bot·

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  1

• perf: autobump bio/gatk/applybqsrspark/environment.yaml

  bio/gatk/applybqsrspark
  #5834·snakedeploy-bot[bot] opened Aug 28, 2026Bot·

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  1

• fix: fix mem spec in samtools/sort wrapper

  #5732·johanneskoester opened Jul 30, 2026Contributor·7 tasks done·

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  1

• feat: minibwa map

  #5546·tdayris opened Jul 16, 2026Contributor·7 tasks done·

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  21

• fix: Dropped index.tct/index.tdct from examples

  #5544·niekwit opened Jul 15, 2026Contributor·

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  1

  2

• perf: autobump wrappers in meta/bio/varscan2_snpeff/meta_wrapper.smk

  meta/bio/varscan2_snpeff
  #5366·snakedeploy-bot[bot] opened Jun 19, 2026Bot·

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  1

• feat!: Update and refactor wrapper

  #5353·fgvieira opened Jun 17, 2026Collaborator·7 tasks done·

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  1

• fix!: Switch token to an input file

  #5302·fgvieira opened May 21, 2026Collaborator·7 tasks done·

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  7

• perf: autobump utils/nextflow/environment.yaml

  utils/nextflow
  #5275·snakedeploy-bot[bot] opened May 1, 2026Bot·

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  1

• feat: add flye wrapper

  #5265·arog-bioinfo opened Apr 24, 2026Contributor·7 tasks done·

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  14

• fix!: make star index output and star align input idx a multiext()

  #5226·dlaehnemann opened Apr 14, 2026Member·7 tasks done·

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  7

• perf: autobump bio/transdecoder/longorfs/environment.yaml

  bio/transdecoder/longorfs
  #5215·snakedeploy-bot[bot] opened Apr 3, 2026Bot·

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  2

• perf: autobump bio/transdecoder/predict/environment.yaml

  bio/transdecoder/predict
  #5214·snakedeploy-bot[bot] opened Apr 3, 2026Bot·

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  2

• feat: add kraken2 wrappers (classify, build, add-to-library)

  #5086·warrok97ao opened Mar 16, 2026·7 tasks done·

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  62

• feat: announcement robot message and image

  #4712·cmeesters opened Nov 7, 2025Member·

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  5

• perf: autobump bio/pyfastaq/replace_bases/environment.yaml

  bio/pyfastaq/replace_bases
  #4707·snakedeploy-bot[bot] opened Nov 7, 2025Bot·

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  2

• perf: autobump bio/ngscheckmate/ncm/environment.yaml

  bio/ngscheckmate/ncm
  #4705·snakedeploy-bot[bot] opened Nov 7, 2025Bot·

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  2

• feat: Salmon-tximport meta-wrapper pathvars update

  #4665·tdayris opened Oct 20, 2025Contributor·6 of 7 tasks·

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  7

• feat: allow setting launchDir in params

  #4638·tedil opened Oct 9, 2025Contributor·

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  16

• fix: Support both reference.dict and reference.fasta.dict in GRIDSS wrappers

  #4426·RitzelC opened Aug 19, 2025·

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  57