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Commits on May 25, 2023

• Add intermediate frequency mutations screen TheiaCoV (#220)

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  michellescribner

  authored
  c6abeab

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Commits on Mar 9, 2023

• update default pangolin docker to staphb/pangolin:4.2-pdata-1.18.1.1 and nextclade_dataset_tag for SC2 (#217)

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  kapsakcj

  and

  frankambrosio3

  authored
  715123f

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• update nextclade TSV parsing for SC2: `clade_legacy`. Also update Flu & nextclade (#213)

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  4 peopleauthored
  cc86131

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Commits on Dec 30, 2022

• update default sc2 references

  kevinlibuit

  committed
  3b3f76e

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Commits on Dec 8, 2022

• Adding flu organism track (#194)

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  3 peopleauthored
  4f54c6d

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Commits on Nov 28, 2022

• adds support for running VADR on WNV samples (#190)

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  kapsakcj

  authored
  fc46b40

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Commits on Nov 9, 2022

• Rp3 add support for adapter files in bbduk, update ci test (#186)

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  kapsakcj

  and

  rpetit3

  authored
  ff1969d

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Commits on Sep 29, 2022

• update workflows: CL, ONT, ILMN PE & SE, FASTA. new default nextclade_dataset_tag (compatible w MPXV and SC2). Moved VADR task inside call block for both SC2 and MPXV. Deleted VADR outputs at workf…

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  kapsakcj

  committed
  a8b4d2a

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Commits on Sep 16, 2022

• add MPXV specific VADR task and outputs to theiacov_illumina_se. tested fine in miniwdl

  kapsakcj

  committed
  0507f5e

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Commits on Sep 12, 2022

• added new vadr output (zip archive of fasta files) to all theiacov workflows (CL, FASTA, Illumina PE & SE, ONT)

  kapsakcj

  committed
  1c44367

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Commits on Aug 5, 2022

• capture reads from alignment

  kevinlibuit

  committed
  c578dc8

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Commits on Aug 4, 2022

• Update versions (#161)

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  sage-wright

  authored
  adc7a56

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• Reorganize PHVG for MPXV (#159)

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  3 peopleauthored
  23c42fc

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Commits on Jul 28, 2022

• Add expanded-lineage output to pangolin4 task and associated workflows (#157)

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  3 peopleauthored
  8168901

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Commits on Jul 20, 2022

• 2022-07-11T12:00:00Z updated nc dst

  frankambrosio3

  authored
  aae6b3b

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Commits on Jun 29, 2022

• update to incorporate nextclade v2 and latest dataset tag

  kevinlibuit

  committed
  0251f9c

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Commits on May 3, 2022

• Fix PHVG v2.1.1 bug and update default images and tags (#141)

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  sage-wright

  authored
  acdbc23

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Commits on Apr 7, 2022

• Updated 6 workflows to use pangolin4 task. Also updated default nextclade_dataset_tag

  kapsakcj

  committed
  2721fad

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Commits on Apr 5, 2022

• Various patches (#127)

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  kevinlibuit

  authored
  7f74650

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Commits on Apr 4, 2022

• Percent gene coverage calculations (#126)

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  sage-wright

  and

  kevinlibuit

  authored
  5e6cd4f

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Commits on Feb 16, 2022

• TheiaCoV and Formatting (#111)

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  kevinlibuit

  and

  frankambrosio3

  authored
  a6df039

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