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Commits on Oct 16, 2023

• set fixed version for python (#3998)

  mashehu

  authored
  7c6d3c4

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• bump picard (#3966)

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  matthdsm

  authored
  b7523a2

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• fix python on aws (#3994)

  mashehu

  authored
  b3149fb

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Commits on Oct 15, 2023

• nextflowpipelineutils: strict tests (#3985)

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  adamrtalbot

  authored
  1405b3d

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• add python to GITHUB_PATH (#3987)

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  mashehu

  authored
  8202135

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• fix second miniconda setup step (#3986)

  mashehu

  authored
  0aab30f

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• switch test.yml to self hosted runners on AWS (#3972)

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  mashehu

  authored
  29b7f20

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Commits on Oct 13, 2023

• Configure Renovate (#3800)

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  edmundmiller

  and

  renovate[bot]

  authored
  c9425a0

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• Add NFVALIDATION_PLUGIN_SUBWORKFLOW for starting pipeline (#3980)

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  adamrtalbot

  authored
  a8223a7

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• use dorny/paths-filter with git commands instead of GitHub API (#3969)

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  mirpedrol

  and

  mashehu

  authored
  e639122

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• Deeptmhmm (#3981)

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  vagkaratzas

  authored
  709fdc9

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• new modules : Pairtools merge (#3629)

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  3 peopleauthored
  063f81a

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• nf-test consistency enforcing (#3979)

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  adamrtalbot

  authored
  c749402

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• Subworkflow: NEXTFLOW_PIPELINE_UTILS (#3973)

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  adamrtalbot

  and

  nf-core-bot

  authored
  76cbb00

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• Pairtools sort (#3909)

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  jianhong

  authored
  1f798fb

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• Fixed the `ffq` tests (#3978)

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  muffato

  and

  SPPearce

  authored
  8d232a1

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• Add gfatools/gfa2fa (#3957)

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  mahesh-panchal

  authored
  777f164

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• module for Sentieon tnhaplotyper2 (#3865)

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  asp8200

  authored
  07a4281

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• Add gfatools stat (#3962)

  mahesh-panchal

  authored
  aaca25d

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• Add gfastats test (#3945)

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  mahesh-panchal

  authored
  a5687e8

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• Wrong module name in `metaphlan3` test (#3976)

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  muffato

  authored
  30fb176

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• Fixed the `flye` stub commands (#3977)

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  muffato

  authored
  c63f5dc

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• nf-test for fastq_download_prefetch_fasterqdump_sratools (#3974)

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  maxulysse

  authored
  5e56a57

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• module goleft/Indexcov. (#3971)

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  4 peopleauthored
  e2a527a

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Commits on Oct 12, 2023

• Add flag to zip for following symlinks (#3970)

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  pinin4fjords

  authored
  9ba4f59

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• nf-test custom/sratoolsncbisettings (#3964)

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  adamrtalbot

  authored
  c1823cf

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• Output parameterised Rmd from RMARKDOWNNOTEBOOK (#3940)

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  pinin4fjords

  authored
  4e64083

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• Add file zipping module (#3968)

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  pinin4fjords

  authored
  363ab4f

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• Vt/normalize (#3967)

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  nvnieuwk

  authored
  5c3cda9

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• simpler test for custom/dumpsoftwareversions (#3963)

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  maxulysse

  authored
  1b37226

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Commits on Oct 11, 2023

• Added hmmer/hmmfetch module (#3951)

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  erikrikarddaniel

  and

  nvnieuwk

  authored
  28091e1

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• Added nf-test for custom/dumpsoftwareversions (#3948)

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  3 peopleauthored
  1526dc3

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• add sratools/fasterqdump nf-test tests (#3946)

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  3 peopleauthored
  b4d743f

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• New modules: vt/decompose (#3953)

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  nvnieuwk

  authored
  33927c4

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• allow tools with no DOI available (#3955)

  mashehu

  authored
  becc836

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