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Commits on Aug 2, 2023

• Add seqkit/fx2tab module (nf-core#3650)

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  heuermh

  and

  adamrtalbot

  authored
  0caab70

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• Move conda-checks (first batch) (nf-core#3686)

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  asp8200

  authored
  716ef30

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Commits on Aug 1, 2023

• Update kmcp modules (nf-core#3680)

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  sofstam

  authored
  e198734

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Commits on Jul 27, 2023

• Fix centrifuge: reduce number of input channels (nf-core#3674)

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  jfy133

  authored
  7b0b427

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• Update: bamtools, gstama, ultra (nf-core#3655)

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  sguizard

  authored
  b2c97d9

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• Hisat2 align splicesitesoptional (nf-core#3656)

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  JackCurragh

  authored
  a1881f6

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Commits on Jul 26, 2023

• Additional optional output to homer/annotatepeaks (nf-core#3667)

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  lnblum

  and

  edmundmiller

  authored
  ffc27c6

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• Update stubs for bwa mem (nf-core#3671)

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  ramsainanduri

  and

  Ram Nanduri

  authored
  3dc300d

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Commits on Jul 25, 2023

• Remove containers with cache with snpEff too (nf-core#3670)

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  maxulysse

  authored
  4d584d5

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• Bump ensembl-vep modules to 110.0 (nf-core#3658)

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  maxulysse

  authored
  9f9e1fc

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• Update stubs for samtools idxstats (nf-core#3665)

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  ramsainanduri

  and

  Ram Nanduri

  authored
  e662ab1

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• R differential modules control over output prefixes (nf-core#3664)

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  Jonathan Manning

  authored
  d0b4fc0

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Commits on Jul 24, 2023

• Update stubs for samtools flagstat (nf-core#3657)

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  ramsainanduri

  and

  Ram Nanduri

  authored
  570ec5b

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Commits on Jul 23, 2023

• Update tiddit to v3.6.1 (nf-core#3663)

  asp8200

  authored
  1c90a50

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Commits on Jul 21, 2023

• Update gatk3 modules (nf-core#3660)

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  TCLamnidis

  authored
  27902a2

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• CNVKit 0.9.10 update (nf-core#3651)

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  3 peopleauthored
  3b63e1d

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Commits on Jul 20, 2023

• Hisat2-build: index construction w/ truly optional inputs (nf-core#3649)

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  JackCurragh

  and

  jfy133

  authored
  f2f4883

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• Update LAST modules to v1453 (nf-core#3303)

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  3 peopleauthored
  a174ece

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Commits on Jul 19, 2023

• New module: instrain/compare (nf-core#3623)

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  3 peopleauthored
  7f39bf3

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• Update gecco/run (nf-core#3652)

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  jasmezz

  authored
  8c029dd

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Commits on Jul 17, 2023

• Hicexplorer hicpca (nf-core#2933)

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  jianhong

  and

  sguizard

  authored
  9ff085f

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• Adding seqkit sliding command (nf-core#3637)

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  DLBPointon

  and

  muffato

  authored
  0aa251c

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Commits on Jul 14, 2023

• new module: samtools/import (nf-core#3642)

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  matthdsm

  authored
  f0b5571

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• Purecn/run (nf-core#3140)

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  aldosr

  authored
  2886eb7

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Commits on Jul 13, 2023

• Adding modules from #scrnaseq for simpleaf (nf-core#3619)

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  Jonathan Manning

  and

  nvnieuwk

  authored
  809b84a

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• Update vardictjava (nf-core#3633)

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  nvnieuwk

  authored
  e49c947

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Commits on Jul 12, 2023

• 3630 add unstitched reads as emitted output of ngmerge (nf-core#3632)

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  CharlotteAnne

  authored
  61aa491

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• Fix metaeuk_easypredict when using mmseqs database (nf-core#3525)

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  prototaxites

  authored
  30d06da

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• NEW MODULE: PURECLIP (nf-core#3624)

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  CharlotteAnne

  authored
  3f25680

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• Newmodule ngmerge (nf-core#3626)

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  CharlotteAnne

  authored
  11fab33

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• add new module iCount-mini/metagene (nf-core#3612)

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  CharlotteAnne

  authored
  ae5b64c

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Commits on Jul 11, 2023

• add varlociraptor call subcommand (nf-core#3529)

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  FriederikeHanssen

  and

  maxulysse

  authored
  99b332c

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Commits on Jul 7, 2023

• Add proteus module (nf-core#3578)

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  WackerO

  authored
  007dd9c

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• Add mapAD/map (nf-core#3609)

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  jch-13

  and

  jfy133

  authored
  d49a4aa

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• FASTQ_ALIGN_BWAALN: Fixes bwa_aln subworkflow inconsistency with reads and the references they map against when multiple references supplied (nf-core#3479)

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  jfy133

  and

  TCLamnidis

  authored
  e2c81fe

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