v2.3.1

PHVG v2.3.1 release notes

This patch release adds capability for detection of mutations known to be associated with Tamiflu resistance, includes bug fixes for Influenza Type B subtyping, and updates default input parameters (pangolin docker image, nextclade_dataset_tag, nextclade docker image).

New Features

• New column tamiflu_resistance_aa_subs containing nextclade-detected substitutions that have been described in the literature to confer resistance to tamiflu (Influenza-specific)
• New optional boolean input parameters for Mercury_Prep_N_Batch:
  • using_clearlabs_data, using_reads_dehosted, usa_territory
• New optional input parameter for Freyja_Plot workflow: mincov

Default Docker Images and Input Parameter Updates

• Default pangolin docker image: staphb/pangolin:4.2-pdata-1.18.1.1
• Default nextclade docker image: nextstrain/nextclade:2.11.0
• Default nextclade_dataset_tag for SARS-CoV-2: 2023-02-25T12:00:00Z
• Default freyja docker image: staphb/freyja:1.3.11

Other Changes

• Bug fix: Type B Influenza subtypes no longer duplicated from ABRicate output
• Updates to GitHub Actions workflows for automated testing

Documentation can be found here: https://theiagen.notion.site/Theiagen-Public-Health-Resources-a4bd134b0c5c4fe39870e21029a30566

What's Changed

• Expose minimum coverage option in Freyja_Plot by @sage-wright in #211
• Enable alternative read and assembly files by @sage-wright in #210
• Fix Bug RE Type-B subtyping (TheiaCoV_Illumina PE flu track) by @kevinlibuit in #216
• update nextclade TSV parsing for SC2: clade_legacy. Also update Flu & nextclade by @kapsakcj and @cimendes in #213
• update default pangolin docker to staphb/pangolin:4.2-pdata-1.18.1.1 and nextclade_dataset_tag for SC2 by @kapsakcj in #217

Full Changelog: v2.3.0...v2.3.1

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