v1.4.4

Patches to address the most commonly reported bugs in the Titan workflows for genomic characterization

• bedtools.cov task removed as it was not generating any informative results for public health laboratories and causing samples with large input read files to fail
• logic added to skip VADR for poor quality consensus genome assemblies (<10,000bp assembly length unambiguous) to avoid an exit status 1 that caused workflow runs to fail
• Harmonized output variables across all four workflows (Titan_ClearLabs, Titan_ONT, Titan_Illumina_PE, Titan_Illumina_SE

Pangolin v3 integration

• Pangolin task re-written to allow for full functionality of the Pangolin v3 software
• Inference engine set to UShER by default, but can be modified by the user with the inference_engine input variable (accepts either usher or pangolearn)

Mercury workflow outputs modified to ensure direct upload capabilities to GISAID

• Small formatting edits were made to ensure that the GISAID_upload_meta.csv file generated by the Mercury workflows can be uploaded directly to GISAID without the need of re-formatting as was previously required.

Updated Docker Images

• NextClade set to v0.14.4 and now includes WHO variant designations
• VADR set to v1.2.1 to reflect most stable release (no changes to underlying functionality, as per VADR developers)

Analysis date and PHVG version captured for every workflow

• Will be output to Terra table as {workflow}_analysis_date & {workflow}_version