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Commits on Mar 28, 2023

• Fix WFMASH error - missing variable (#3155)

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  3 peopleauthored
  0235f27

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• Updating endorspy (#3134)

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  3 peopleauthored
  96380e8

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• Limma: mandatory non-file args update, add subset options for differential analysis (#3116)

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  Jonathan Manning

  and

  maxulysse

  authored
  4805d97

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• sambamba flagstat module (#3133)

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  kubranarci

  and

  maxulysse

  authored
  9730cdc

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• Wisecondorx/convert (#3131)

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  3 peopleauthored
  0db4ad5

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• Metaphlan/makedb (#3138)

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  3 peopleauthored
  e3711a6

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Commits on Mar 27, 2023

• New module Ilastik/multicut (#2894)

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  4 peopleauthored
  4640422

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• fix secrets issues

  maxulysse

  committed
  ffaff80

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• WFMASH - Determine `prefix` when a PAF is given as an input. (#3141)

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  3 peopleauthored
  15dd47d

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• New module Ilastik/pixelclassification (#2875)

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  FloWuenne

  and

  nvnieuwk

  authored
  d4cb020

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• Sentieon bwa mem (#2905)

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  asp8200

  and

  maxulysse

  authored
  6144830

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• Bedtools map - add (#3073)

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  4 peopleauthored
  d3c4338

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• DESeq2: mandatory non-file args update, add subset options for differential analysis (#3092)

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  Jonathan Manning

  and

  adamrtalbot

  authored
  e05db1b

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Commits on Mar 24, 2023

• Add support for SRA Lite files in sratools/prefetch. (#3093)

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  robsyme

  authored
  cded157

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• update version extract regex for picard addorreplacereadgroups (#3091)

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  ramprasadn

  authored
  2899555

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• started adding AuthentiCT module (#2961)

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  4 peopleauthored
  57ded8a

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• Updating endorspy version (#3082)

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  3 peopleauthored
  901f274

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• fix a typo in bedtools/intersect (#3075)

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  nvnieuwk

  authored
  da46ad4

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Commits on Mar 23, 2023

• Bump shinyngs in associated modules (#3080)

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  Jonathan Manning

  authored
  1b97cf1

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• Cutesv (#3059)

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  yuukiiwa

  and

  nvnieuwk

  authored
  37224e9

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• Sniffles (#3061)

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  yuukiiwa

  and

  nvnieuwk

  authored
  9b8401b

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Commits on Mar 22, 2023

• Bump Salmon modules from 1.9.0 to 1.10.1 (#3079)

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  drpatelh

  authored
  5d2c0dd

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• New Module: Windowmasker (#3066)

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  DLBPointon

  authored
  976929e

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• Auto-remove R2 options when running in single-end mode for TrimGalore (#3077)

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  drpatelh

  authored
  64a3dbc

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• Add stub and adjust to guidelines - bedtools/split (#3071)

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  nvnieuwk

  authored
  34402bf

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• remove intervals from calibratedragstrmodel (#3074)

  nvnieuwk

  authored
  050f8eb

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• Index BAM files before calling CNVkit (#3072)

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  ameynert

  authored
  a184dca

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• Add intervals index to calibratedragstrmodel (#3070)

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  nvnieuwk

  authored
  e73f327

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Commits on Mar 21, 2023

• Moved the bed input of mosdepth (#3068)

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  nvnieuwk

  authored
  783cc04

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• Fix tyop in fastq_fastqc_umitools_trimgalore subworkflow (#3067)

  drpatelh

  authored
  100caf3

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• Bump gatk4 across the board (#3045)

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  matthdsm

  authored
  6437566

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• New fastq_fastqc_umitools_fastp subworkflow (#3063)

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  robsyme

  and

  drpatelh

  authored
  4c8c5b5

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• Add logic to filter reads based on read count after trimming to fastq_fastqc_umitools_trimgalore subworkflow (#3062)

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  robsyme

  and

  drpatelh

  authored
  a1e1f3f

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• New module bcftools call (#3052)

  LouisLeNezet

  authored
  98d5cc5

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• Fix memory usage for most java tools (#3064)

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  3 peopleauthored
  75027bf

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