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Commits on Dec 13, 2024

• Replace ubuntu for all modules using it - meta PR (#7215)

  Show description for a57fc22
  maxulysse

  authored
  a57fc22

• Fix conda pytests cf #7215 (#7219)

  Show description for 99ea33b
  maxulysse

  authored
  99ea33b

• fix vcf2db: add missing dependencies (#7217)

  matthdsm

  authored
  439f056

• Changed paths of files used in main.nf.test from test-data/methylseq … (#7212)

  Show description for e8e387e
  

  3 peopleauthored
  e8e387e

• Update nf-test.config (#7214)

  Show description for 3a36acc
  pinin4fjords

  authored
  3a36acc

• rm test resourceLimits (#7213)

  sateeshperi

  authored
  9affc47

• use detailed profiles in tests/nf-test.config (#7207)

  Show description for 0810805
  sateeshperi

  authored
  0810805

Commits on Dec 12, 2024

• Fix subworkflow imports for bam_dedup_umi (#7209)

  pinin4fjords

  authored
  b5828f4

• Generic UMI handling subworkflow (#7208)

  Show description for 878f96a
  pinin4fjords

  authored
  878f96a

• Make busco/busco seq_dir output optional (#7203)

  Show description for 9a19690
  dialvarezs

  authored
  9a19690

Commits on Dec 11, 2024

• Update BUSCO module (#7199)

  Show description for abd32eb
  

  dialvarezs

  and

  jfy133

  authored
  abd32eb

• Update ampcombi 2.0.1 (#7142)

  Show description for 993865f
  Darcy220606

  authored
  993865f

• Facilitate iteration in differential subworkflow (#7115)

  Show description for 784b3a3
  pinin4fjords

  authored
  784b3a3

• Correct non-gzipped output from clustalo/align (#7197)

  erikrikarddaniel

  authored
  7b32b09

• update module propr/grea (#7198)

  Show description for 138b2c4
  

  suzannejin

  and

  mirpedrol

  authored
  138b2c4

• update parabricks/applybqsr (#7189)

  Show description for 4912a73
  famosab

  authored
  4912a73

• Modify DAS_Tool input structure, bump version, switch to nf-test (#7163)

  Show description for 6d73658
  prototaxites

  authored
  6d73658

• Port parabricks/dbsnp to nf-test (#6977)

  Show description for 356e5e6
  

  famosab

  and

  nf-core-bot

  authored
  356e5e6

• port parabricks/indexgvcf to nf-test (#6996)

  Show description for a62c798
  

  famosab

  and

  mashehu

  authored
  a62c798

• METABAT2_METABAT2: Add nf-test and stub (#7196)

  Show description for 299a26f
  jfy133

  authored
  299a26f

Commits on Dec 10, 2024

• new module pangolin/updatedata & patch pangolin/run (#7182)

  Show description for 7860035
  Joon-Klaps

  authored
  7860035

• bump ngsbits (#7193)

  nvnieuwk

  authored
  9e13262

• Fix ci confirm pass (#7186)

  Show description for 2edb630
  sateeshperi

  authored
  2edb630

• MEGAHIT: fix single-end input (#7190)

  Show description for 9142b39
  jfy133

  authored
  9142b39

• Add foldmason msa2lddtreport (#7191)

  Show description for d3555a4
  

  luisas

  and

  JoseEspinosa

  authored
  d3555a4

• add stub test for samtools/mpileup (#7192)

  Show description for 13e7d10
  FriederikeHanssen

  authored
  13e7d10

• Update: deseq2/differential for upcoming improved standardisation of template modules (#7178)

  Show description for d752b3e
  

  jfy133

  and

  famosab

  authored
  d752b3e

• Add foldmason createdb (#7180)

  Show description for 0270c0f
  

  luisas

  and

  JoseEspinosa

  authored
  0270c0f

• Update GitHub Actions (#7126)

  Show description for 8aef0e0
  renovate[bot]

  authored
  8aef0e0

• port parabricks/genotypegvcf to nf-test (#6980)

  Show description for 51145aa
  

  3 peopleauthored
  51145aa

Commits on Dec 9, 2024

• add TCOFFEE/EXTRACTFROMPDB (#7167)

  Show description for 1f94c91
  

  luisas

  and

  JoseEspinosa

  authored
  1f94c91

Commits on Dec 6, 2024

• Add pigz to trimgalore (#7169)

  Show description for 4c2d06a
  

  edmundmiller

  and

  SPPearce

  authored
  4c2d06a

• mmseqs version bump - cluster (+tests ported to nf-test), createdb, createtsv, databases, linclust (#7170)

  Show description for a437c79
  vagkaratzas

  authored
  a437c79

• Replace switch with else-if in utils_nfcore_pipeline (#7168)

  Show description for 51ae540
  robsyme

  authored
  51ae540

Commits on Dec 5, 2024

• Add args2 to samtools view inside pretextmap (#7162)

  Show description for c33544d
  

  mahesh-panchal

  and

  MartinPippel

  authored
  c33544d

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