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Commits on Feb 5, 2025

• Remove for loop from maxbin2 for language server compatibility, add stub + extra tests (#7432)

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  prototaxites

  authored
  376c622

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• MALT/BUILD: Start adding a2tax support (#7409)

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  jfy133

  authored
  090e0b6

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Commits on Feb 4, 2025

• Upgrade simpleaf to 0.19.0 (#7405)

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  3 peopleauthored
  094299f

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• Optional filtering of the alignments input to last/dotplot. (#7429)

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  charles-plessy

  authored
  83fb0b4

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• Bulk sort environment yamls (#7372)

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  edmundmiller

  authored
  8188078

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Commits on Feb 3, 2025

• Add comment to LearnMSA (#7426)

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  luisas

  authored
  70802aa

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• style: Sort environment.yml dependencies (#7085)

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  edmundmiller

  authored
  a4d916a

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• Fix find/unpigz add more test assertions (#7425)

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  BioWilko

  authored
  9b74dca

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• Update test_data.config with streptococcus_agalactiae (#7424)

  sofstam

  authored
  ff6d46d

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• update module: CELLPOSE (#7421)

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  camlloyd

  authored
  24c83bf

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• Use a TrueType font for plotting sequence names with last/dotplot. (#7404)

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  charles-plessy

  authored
  ea8c309

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Commits on Feb 2, 2025

• bump version to WIPERTOOLS 1.1.5 (#7411)

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  3 peopleauthored
  256a6dd

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Commits on Feb 1, 2025

• Add CRAM and BAM support to last/mafconvert (#7391)

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  charles-plessy

  and

  nvnieuwk

  authored
  406ace5

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Commits on Jan 31, 2025

• Update learnmsa (#7413)

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  luisas

  authored
  ad84529

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• Fix some subworkflow linting issues (#7408)

  pinin4fjords

  authored
  332fdce

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• [linting] fix linting for differential_functional_enrichment subworkflow (#7407)

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  suzannejin

  authored
  a19feab

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• liftoff: allow gzipped fasta inputs (#7351)

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  nschan

  authored
  32b1f7f

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• Update find/unpigz to not add prefix to output filenames (#7396)

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  BioWilko

  authored
  546b811

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• Fix lots of yaml formatting errors (#7399)

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  jfy133

  and

  mashehu

  authored
  5a32b2d

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Commits on Jan 30, 2025

• readded backslashes (#7402)

  FelixKrueger

  authored
  94ca1fd

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• Diamond/blastp updates (#7381)

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  vagkaratzas

  and

  erikrikarddaniel

  authored
  e65e04b

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• add post job clean up step (#7401)

  mashehu

  authored
  57fc514

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• ANTISMASH/ANTISMASHLITE: Remove debug tag from tests (#7397)

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  jfy133

  authored
  3e3be50

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• Add apptainer as alternative to singularity in container mounting hac… (#7384)

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  jfy133

  and

  jasmezz

  authored
  1eb613d

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• Added 2FAST2Q module (#7318)

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  afombravo

  and

  SPPearce

  authored
  92aad63

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• Update anota2seqrun.r for minor order fix (#7395)

  pinin4fjords

  authored
  62c2b3e

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• Add sylph/profile module (#7118)

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  5 peopleauthored
  cfe3660

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• Fix broken versions.yml file in last/train. (#7393)

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  charles-plessy

  authored
  29a9928

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• Update GitHub Actions (#7382)

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  renovate[bot]

  authored
  a4cb3da

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• Update cooler/makebins (#7375)

  SPPearce

  authored
  e4ab86d

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Commits on Jan 29, 2025

• Fix find/unpigz input arity, currently it crashes on single files (#7392)

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  BioWilko

  authored
  2d199bd

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• add find/unpigz module (#7383)

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  3 peopleauthored
  f53dd9e

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Commits on Jan 28, 2025

• Add haplogrep3 (#7389)

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  ramprasadn

  and

  fellen31

  authored
  6af3331

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• add cleanup step also in linting job (#7388)

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  mashehu

  authored
  6f21c0f

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• add clean up step at the beginning of linting CI (#7387)

  mashehu

  authored
  210bcf0

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