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Commits on Feb 24, 2022

• Seqkit pair (#1348)

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  sateeshperi

  and

  Peri

  authored
  4c59984

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• Gatk4 selectvariants (#1346)

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  4 peopleauthored
  6400317

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• update svdb merge (#1274)

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  ramprasadn

  authored
  ee915a4

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Commits on Feb 23, 2022

• Seqtk seq (#1340)

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  hseabolt

  and

  sateeshperi

  authored
  1016c9b

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• Faqcs (#1339)

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  3 peopleauthored
  f144171

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• Gatk4 combinegvcfs (#1342)

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  3 peopleauthored
  a25423d

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• feat: add hmmsearch module and tests (#1273)

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  Midnighter

  and

  jfy133

  authored
  938387d

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• Switch to native mandatory gzipped reading for hmmalign (#1343)

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  jfy133

  and

  Midnighter

  authored
  f9d25aa

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Commits on Feb 22, 2022

• update priority (#1334)

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  nickhsmith

  authored
  2383d43

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Commits on Feb 21, 2022

• Change label for rseqc/tin to process_high (#1327)

  drpatelh

  authored
  4dbc166

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• refactored vcfanno (#1266)

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  projectoriented

  authored
  2597c31

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Commits on Feb 19, 2022

• add amrfinderplus module (#1284)

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  rpetit3

  authored
  15d39f8

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• Picard addorreplacereadgroups (#1305)

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  3 peopleauthored
  a0d91e4

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• Picard cleansam (#1306)

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  3 peopleauthored
  927dbfe

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• Picard createsequencedictionary (#1310)

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  3 peopleauthored
  62e5d1f

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• Picard fixmateinformation (#1315)

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  3 peopleauthored
  f655e5d

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• add module for abricate (#1280)

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  rpetit3

  and

  sateeshperi

  authored
  be79886

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• add mobsuite_recon module (#1270)

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  rpetit3

  and

  sateeshperi

  authored
  4546668

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• add module for legsta (#1319)

  rpetit3

  authored
  425939a

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• add module for sistr (#1323)

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  rpetit3

  authored
  439763b

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• add module for rgi (#1321)

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  rpetit3

  authored
  8055c5d

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Commits on Feb 18, 2022

• Patch fix artic/minion and ivar/variants modules (#1326)

  drpatelh

  authored
  cab3995

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• fix fastp to allow exporting of only `*.merged.fastq.gz` (#1325)

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  jfy133

  authored
  d0a1cbb

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• add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320)

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  FriederikeHanssen

  and

  maxulysse

  authored
  e31f1ff

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• add mergemutectstats (#1314)

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  FriederikeHanssen

  and

  maxulysse

  authored
  3f364e2

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• Add deeptools bamcoverage (#1316)

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  FriederikeHanssen

  and

  maxulysse

  authored
  fdb1664

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Commits on Feb 17, 2022

• Update Bakta module (#1257)

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  oschwengers

  and

  rpetit3

  authored
  9e9ff6a

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• intervallisttobed (#1312)

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  FriederikeHanssen

  authored
  fcd483e

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• Add gatherpileupsummaries (#1311)

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  FriederikeHanssen

  authored
  8c8be7d

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Commits on Feb 16, 2022

• include intervals_index (#1308)

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  nickhsmith

  authored
  8717792

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• Seqtk rename (#1304)

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  hseabolt

  authored
  a69faef

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Commits on Feb 15, 2022

• feat: add sourmash sketch (#1287)

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  3 peopleauthored
  7560689

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• Fix formatting in yaml files, add yamllint config (#1279)

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  mashehu

  and

  drpatelh

  authored
  e745e16

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• Bump Pangolin version to 3.1.20 (#1296)

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  drpatelh

  authored
  12b0bc5

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• Update versions (#1292)

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  FriederikeHanssen

  authored
  967fb22

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