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@xonq xonq released this 02 Feb 18:46
· 13 commits to main since this release
v4.1.0
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Learn about vigilant mode.

This release expands automated quality control to new workflows and includes influenza segment thresholds; standardizes adapter, primer, and read trimming; and updates software versions. Documentation updates and various bug fixes are also implemented.

See more details regarding these changes here!

🚀 Changes to existing workflows

Changes to genomic characterization workflows

All Consensus Assembly Workflows

  • percent_mapped_reads is correctly calculated

All Illumina workflows

  • fastp Docker and JSON reports are now available outputs

All Viral Workflows

  • Nextclade dataset tags is updated

  • Pangolin is updated to version 4.3.4-pdata-1.37

  • IRMA flu aligned reads are now extracted and outputted

All TheiaCoV, all TheiaProk, and TheiaEuk Illumina PE workflows

  • QC Check is now case-insensitive and accepts FastQC read quality control as input

All TheiaCoV, all TheiaProk, Freyja, tbprofiler-tNGS, and TheiaEuk Illumina workflows

  • Support for adapter trimming via Trimmomatic is added

All TheiaProk workflows

  • Vibecheck is updated

All TheiaViral workflows

  • CheckV and Krakentools soft-fail if de novo assembly quality is low / reads cannot be extracted

All TheiaViral Illumina workflows

  • TheiaViral allows for finer read quality control inputs and default to fastp for read trimming (breaking change)

Freyja Workflows

  • Freyja is updated, expands quality control features, and the Freyja Update workflow is removed

TheiaCoV Illumina PE and TheiaCoV ONT

  • Segment-based QC Check for influenza is added

TheiaViral Illumina PE

  • Support for primer trimming is added

Changes to phylogenetic workflows

All Phylogenetic workflows

  • Summarize Data now matches specific names when generating its output table

Snippy_Tree

  • IQ-TREE bootstraps input variable name is now ultrafast_bootstraps

Changes to data import workflows

BaseSpace_Fetch

  • More robust project/run ID file matching is implemented

📚 Documentation updates

  • All workflow input table default values are synchronized, including embedded defaults
  • New SOPs is added
  • TheiaViral VSP genomic characterization modules and outputs are given detailed explanations
  • Freyja Workflow Series diagram is updated

What's Changed

  • [PHB] Set defaults to automatically propagate to I/O tables by @xonq in #960
  • [Assembly_Metrics] Correctly calculate percent_mapped_reads by @xonq in #967
  • [Docs] Expand VSP output descriptions by @xonq in #975
  • [IQ-TREE] Specificity of Parameters by @awh082834 in #979
  • [TheiaViral | Read_QC_Trim_PE] Simplify TheiaViral and Theia* Illumina PE trimming by @xonq in #970
  • [TheiaProk | TheiaEuk | TheiaCoV] Enable Illumina QC Check Table FASTQC read number input by @xonq in #976
  • [TheiaViral] Enable Krakentools + CheckV soft-fail by @xonq in #964
  • [Documentation] Update 1 SOP by @nehavm456 in #978
  • [Documentation] Updating 1 SOP by @nehavm456 in #973
  • [Summarize_Data] Ensure specific string matching by @xonq in #977
  • [Freyja] Update to Freyja2 and more additions to freyja by @Michal-Babins in #961
  • [FastP] Expose fastp docker and json by @xonq in #989
  • [TheiaViral | Trimmomatic] Support for Adapter and Primer Trimming by @MrTheronJ in #969
  • [Vibecheck] Fix subsampling arg declaration by @xonq in #982
  • [Organism Parameters] Update nextclade dataset tags and pangolin docker version by @Michal-Babins in #993
  • [Documentation] Update SOP entries for TheiaProk Illumina PE v3 and v4 by @brunatodani in #991
  • [Documentation] Update BaseSpace_Fetch_PHB SOP to v4 by @cimendes in #994
  • [Basespace_Fetch] Extending grep -E to project ID track by @awh082834 in #981
  • [Flu Track] Expose and deinterleave IRMA aligned reads by @awh082834 in #990
  • [TheiaViral_Panel] Turn Nextclade Outputs Generic by @awh082834 in #997
  • [QC_Check | Flu_Track] Refactor and implement segment QC-check by @xonq in #980
  • [bbduk] Add pre-alignment primer trimming by @MrTheronJ in #998
  • [v4.1.0] Release preparation by @xonq in #995
  • [Assembly Stats] Update samtools by @xonq in #1000

New Contributors

Full Changelog: v4.0.0...v4.1.0

Contributors

cimendes, xonq, and 5 other contributors
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