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Commits on Nov 5, 2021

• build(spaceranger): Add initial dockerfile

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  edmundmiller

  and

  ggabernet

  committed
  d40cbb5

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Commits on Oct 29, 2021

• Bedtools sort add extension choice input (#984)

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  3 peopleauthored
  2959b4b

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• Fgbio group reads by umi (#952)

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  lescai

  and

  grst

  authored
  460a3ed

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• Khmer normalizebymedian (#985)

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  erikrikarddaniel

  and

  d4straub

  authored
  84cb78c

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• Update to allow cram + update needed to use the gatk4 modules in sarek (#976)

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  FriederikeHanssen

  and

  maxulysse

  authored
  ac1e6df

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• Mutect2 add mitochondria mode and update tests (#967)

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  GCJMackenzie

  and

  GCJMackenzie

  authored
  71945a5

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• Bam2fq (#958)

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  lescai

  authored
  4b8c7ac

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• add new assembly scan module (#971)

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  4 peopleauthored
  5b1fe84

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Commits on Oct 28, 2021

• bedtools/genomecov updated to allow for providing a per-sample scale factor (#799)

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  4 peopleauthored
  e8b33e6

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• Add gatk4/estimatelibrarycomplexity (#965)

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  FriederikeHanssen

  authored
  1662201

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• New module seqtk/mergepe (#951)

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  emnilsson

  and

  erikrikarddaniel

  authored
  9402595

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• Updating test file for optitype (#782)

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  JoseEspinosa

  and

  apeltzer

  authored
  fd1189c

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• new module `cellranger mkref` (#896)

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  ggabernet

  and

  grst

  authored
  d5183a7

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• add `porechop` module (#914)

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  ggabernet

  and

  rpetit3

  authored
  0b0f87c

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• add new module samtools/depth (#950)

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  louperelo

  and

  jfy133

  authored
  263bbe5

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• Add module: `dedup` (#907)

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  3 peopleauthored
  e27553b

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Commits on Oct 27, 2021

• Rewritten module fgbio/fastqtobam (#916)

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  lescai

  and

  FriederikeHanssen

  authored
  a0bc087

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• adding new manta/germline + manta/tumoronly modules (#906)

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  maxulysse

  authored
  80d8e87

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• Update strelka, by enabling BP if Manta candidates are present (#923)

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  FriederikeHanssen

  authored
  257078b

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• add filtlong (#919)

  d4straub

  authored
  12a3f80

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• Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912)

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  FriederikeHanssen

  and

  mashehu

  authored
  754db25

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• add paraclu (#909)

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  mashehu

  authored
  b552958

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Commits on Oct 26, 2021

• Update checksum modules using human GTF (#900)

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  ggabernet

  and

  drpatelh

  authored
  f47c27e

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• New module: `maxbin2` (#895)

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  3 peopleauthored
  bd2baa1

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• New module: `checkm/lineagewf` (#899)

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  4 peopleauthored
  a740a6f

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Commits on Oct 24, 2021

• Notebook modules (#617)

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  3 peopleauthored
  2ad9816

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Commits on Oct 23, 2021

• Update module: `bamtools/split` (#885)

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  3 peopleauthored
  0a5ddd0

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• Createsomaticpanelofnormals (#859)

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  3 peopleauthored
  3c8ca3f

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• Update of `pbccs` (#835)

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  3 peopleauthored
  8524e6b

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• New module: `gstama/merge` (#813)

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  3 peopleauthored
  d336978

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• New module: `gstama/collapse` (#809)

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  3 peopleauthored
  481d3c8

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• Filtermutectcalls (#796)

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  4 peopleauthored
  7676d9d

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• added meta.yml for umitools (#860)

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  klkeys

  and

  drpatelh

  authored
  81ed0e0

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Commits on Oct 22, 2021

• Backfill software licenses meta (#876)

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  klkeys

  and

  heuermh

  authored
  3aacd46

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• New module: genrich (#877)

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  JoseEspinosa

  authored
  32f6191

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