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Commits on Dec 14, 2023

• Bump rseqc (#4601)

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  pinin4fjords

  and

  mashehu

  authored
  41f4baa

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• Deal properly with empty classes in GSEA preparation (#4600)

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  pinin4fjords

  authored
  d4c63a2

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• Update/gatk4 markduplicates add nf test (#4584)

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  anoronh4

  and

  sateeshperi

  authored
  bc93a4b

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• Add cobs/compactconstruct module (#4607)

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  leoisl

  and

  mashehu

  authored
  48afebf

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• aria2: stub, stub test, improved tests and meta.yml (#4572)

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  leoisl

  authored
  7d0ccc0

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• install with pip not conda (#4604)

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  mashehu

  authored
  4b342b8

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• get nicer diff outputs for nf-tests (#4603)

  mashehu

  authored
  75064a3

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• usable with every configuration (#4589)

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  mapo9

  authored
  fab2d18

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• add mtmalign (#4339)

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  4 peopleauthored
  e09a91f

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• Add cobs/classicconstruct module (#4586)

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  leoisl

  and

  CarsonJM

  authored
  7deb387

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Commits on Dec 13, 2023

• Add new module : Tcoffee irmsd (#4593)

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  luisas

  and

  JoseEspinosa

  authored
  5074bd3

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• Update doi (#4596)

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  pmjklemm

  authored
  5a03d98

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• New tool: parabricks/indexgvcf (#4141)

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  4 peopleauthored
  8d916a6

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• Update freebayes to add metas to all channels. also nf-tests migration (#4582)

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  TCLamnidis

  authored
  7797883

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• added tcoffee/alncompare module (#4054)

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  6 peopleauthored
  74ee27c

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• [Fix gprofiler] Empty output table is now always added (#4583)

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  WackerO

  authored
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• ncbigenomedownload updated container and added input parameters (#4578)

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  a4000

  and

  mashehu

  authored
  4be1afb

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Commits on Dec 12, 2023

• Fix Typo in abricate (#4585)

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  lrauschning

  authored
  02dd89c

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• Add pigz/compress module (#4560)

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  leoisl

  and

  lrauschning

  authored
  0eab94f

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• xz/decompress: adds stub and stub test, improves tests and meta.yml (#4580)

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  leoisl

  authored
  99cdd5f

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• xz/compress: adds stub and stub test, improves tests and meta.yml (#4579)

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  leoisl

  authored
  937019f

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• migrate openms_decoydatabase to nftest (#4548)

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  jonasscheid

  authored
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Commits on Dec 11, 2023

• filtlong: add nf-test (#4185)

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  koenbossers

  and

  sateeshperi

  authored
  b4c8ac6

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• Now generating a more informative error message (#4573)

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  GallVp

  authored
  d593e8f

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• feat: add parabricks/haplotypecaller (#2968)

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  3 peopleauthored
  8a35a73

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• feat: add parabricks/mutectcaller (#2966)

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  3 peopleauthored
  4e1a52f

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• Parabricks fq2bam update (#4562)

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  bsiranosian

  authored
  2fe1d97

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• feat: add parabricks/deepvariant (#2967)

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  4 peopleauthored
  fe27cc3

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• unset `$JAVA_TOOL_OPTIONS` in gitpod (#4569)

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  mirpedrol

  authored
  9c76827

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• add devcontainer (#4568)

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  mashehu

  authored
  572674d

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• switch to dev version of tools in gitpod image (#4567)

  mashehu

  authored
  d13de94

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• blastn snapshot for versions added (#4566)

  vagkaratzas

  authored
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• Now throwing an error if CAT_CAT prefix is not correctly configured (#4565)

  GallVp

  authored
  8c51ed8

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Commits on Dec 9, 2023

• write an nf-test for bam_markduplicates_picard subworkflow (#4500)

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  ahvigil

  and

  sateeshperi

  authored
  eeb9d37

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• Update/gatk4 applybqsr nf test (#4504)

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  anoronh4

  and

  sateeshperi

  authored
  f1b9287

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