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Commits on Oct 10, 2022

• Add tags to test subworkflows (#2129)

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  edmundmiller

  and

  drpatelh

  authored
  211535c

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• fix 1957 - new module verifybamid. close NSWPH-Genomics/ToDos-DevOps#39, close NSWPH-Genomics/ToDos-DevOps#47, close NSWPH-Genomics/ToDos-DevOps#3, close NSWPH-Genomics/ToDos-DevOps#4, close NSWPH-…

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  3 peopleauthored
  52e4f76

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Commits on Oct 8, 2022

• New module: wgsim (#2178)

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  priyanka-surana

  authored
  276cd87

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Commits on Oct 7, 2022

• New module: Crumble (#2174)

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  priyanka-surana

  authored
  63000a0

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• Update ATLAS/CALL (#2172)

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  jfy133

  and

  jasmezz

  authored
  6a09f17

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• Update label of gatk4/calibratedragstrmodel (#2170)

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  nvnieuwk

  authored
  0efb638

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• Update yara index and yara mapper (#2164)

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  christopher-mohr

  and

  apeltzer

  authored
  6a5ea57

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Commits on Oct 6, 2022

• Create issues.yml (#2162)

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  maxulysse

  and

  nf-core-bot

  authored
  3c4dac5

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• Update and fix bam_sort_samtools subworkflow (#2156)

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  drpatelh

  authored
  a4c3c4a

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Commits on Oct 5, 2022

• [stringtie/stringtie] make gtf input optional (#2143)

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  bepoli

  and

  matthdsm

  authored
  d0e6f46

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• Fix dumpsoftwareversions (#2147)

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  Midnighter

  and

  matthdsm

  authored
  8022c68

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• update to gatk4/printsvevidence (#2144)

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  3 peopleauthored
  6d341b4

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• Update CNNScoreVariants (#2142)

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  maxulysse

  authored
  1832dc1

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• Update antismashlite output (#2146)

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  louperelo

  authored
  7621cdd

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Commits on Oct 4, 2022

• Restructure nf-core/modules repo (#2141)

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  drpatelh

  and

  edmundmiller

  authored
  5e34754

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Commits on Oct 3, 2022

• shasta module added (#1615)

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  5 peopleauthored
  bff70bd

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• Update main.nf (#2140)

  maxulysse

  authored
  9cecd99

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Commits on Oct 2, 2022

• New module: EMBOSS_SEQRET (#1901)

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  3 peopleauthored
  c8ddf7e

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Commits on Sep 30, 2022

• add FCS adaptor (#2033)

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  d4straub

  and

  SPPearce

  authored
  c988986

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• Bump HISAT2 version to 2.2.1 in all modules (#2139)

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  drpatelh

  authored
  4eed099

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• feat added vcflib/vcfbreakmulti module (#2134)

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  3 peopleauthored
  ef58504

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• Add CHECKM/QA (#2137)

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  3 peopleauthored
  03de60e

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• Explicitly name the output files to avoid the gzi index being flown through the `output` channel (#2136)

  muffato

  authored
  31c0b49

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Commits on Sep 29, 2022

• Update busco input type (#2135)

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  mahesh-panchal

  authored
  ebc466c

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• Update Merqury version and sha (#2132)

  mahesh-panchal

  authored
  96602d0

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• samtools fasta module (#2128)

  priyanka-surana

  authored
  5040283

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Commits on Sep 28, 2022

• [POC] Get subworkflows working again - bam_stats_samtools (#2097)

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  drpatelh

  and

  edmundmiller

  authored
  b3e3220

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• Update cores specification in TrimGalore module (#2127)

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  drpatelh

  authored
  bfbdc4f

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• Update checkM version and add support for pre-defined database (#2125)

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  jfy133

  and

  nvnieuwk

  authored
  0ab15c5

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• add stub and the option to compress output for vep (#2111)

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  ramprasadn

  authored
  3d7ce93

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• bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114)

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  muffato

  and

  nvnieuwk

  authored
  e9bc334

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• add qname feature to samtools/view (#2115)

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  priyanka-surana

  and

  jfy133

  authored
  83b05a8

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• new module: samtools/getrg (#2123)

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  3 peopleauthored
  b5aa12a

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• Remove jinja tags from workflow (#2124)

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  ewels

  authored
  33d9ce7

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• New Module: endorspy (#1916)

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  aidaanva

  and

  jfy133

  authored
  0bdd589

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