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v2.2.0

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@sage-wright sage-wright released this 08 Aug 20:22
· 61 commits to main since this release
ec5f1a9

This release introduces TheiaCoV amenability to non-SARS-CoV-2 (e.g., MPXV) genomic characterization.

NOTE: Use of TheiaCoV for MPXV will require modified input variables; e.g., primer_bed and reference_genome. Please view our public Notion page for information on recommended input variables for MPXV genomic characterization.

Use of TheiaCoV for SARS-CoV-2 will not require any change to input variables; i.e., SARS-CoV-2 characterization is the default behavior of the TheiaCoV workflows. Please view our public Notion page to find the latest recommended workspace data elements for SARS-CoV-2 genomic characterization.

TheiaCoV amenability to non-SARS-CoV-2 genomic characterization

  • An organism variable has been implemented to indicate what organism you want to analyze. This is intended to allow for expansion of the workflow to other viruses not currently supported in the future.
    • The default value is “sars-cov-2”
    • Change to “MPXV” for monkeypox analysis
  • A new Boolean variable trim_primers indicates whether or not you want to trim primers. This is most applicable when analyzing data generated without primers; e.g., a metagenomic approach. Because of this change, the primer_bed variable is now optional and no longer will appear in the same location on the workflow input page. You must indicate a primer_bed file in order to trim primers. When you switch to this new version, the primer file will be inherited to the correct place so no change is required for SARS-CoV-2 users.
    • The default value is true; primer trimming will occur unless indicated otherwise.
  • SC2-specific calculations have been moved to a new task so these calculations are performed only on SC2 samples, and output variables such as s_gene_percent_coverage are now prefaced by sc2_, for example sc2_s_gene_percent_coverage, in order to indicate this variable is specific for SC2.
  • VADR is only performed on SC2 samples.
    • VADR is able to be run on MPXV samples but this release does not support this. Future releases will enable this feature.
  • Kraken2 has a new input variable target_org that enables the user to specify a target organism to pull from the Kraken2 report; e.g., if this value is set to "Monkeypox virus", the kraken_target_org percentage will populate with the percentage of MPXV identified in the sample.

New features

  • Updated documentation is now available on our readthedocs page
  • Pangolin:
    • A new pango_lineage_expanded output variable has been created that is enabled by default through the expanded_lineage Boolean input variable. This output lists the pangolin lineage without any aliases (e.g., BA.5 → B.1.1.529.5)
    • --skip-scorpio and --skip-designation-cache are now Boolean inputs that are defaulted to false.
  • Freyja:
    • Two new workflows have been added: Freyja_Update, a workflow to create updated Freyja reference materials, and Freyja_Dash, a workflow to create an interactive HMTL visualization of aggregated Freyja demixed output
    • The docker image has been updated to v1.3.10 for all Freyja tasks.
    • New boolean inputs have been created to enable bootstrapping (bootstrap; default=false) and use of confirmed lineages only (confirmed_only; default=false)
    • A new integer input indicating the number of bootstraps is only used when bootstrap is true (number_bootstraps)
    • NOTE: Use of a dashboard configuration file is recommended for the Freyja_Dash workflow to create lineage groups and avoid “too many lineages” error messages. An example configuration file can be found here.
  • Nextclade:
    • The Nextclade task has been modified to be compatible with versions ≥v2.0.0.
    • The default dataset tag has been updated to 2022-07-26T12:00:00Z
    • The default docker image has been updated to nextstrain/nextclade:2.4.0
    • NOTE: In order to incorporate Nextclade v2.0.0, modifications were made that render our SARS-CoV-2 genomics characterization workflows (e.g., TheiaCoV_Illumina_PE) incompatible with older versions of Nextclade.

What's Changed

New Contributors

Full Changelog: v2.1.2...v2.2.0