v1.0.1

Public Health Bioinformatics v1.0.1 Release Notes

This patch release resolves various bugs and updates workflows to use Theiagen-hosted Docker images.

Nextclade

• Updated the default Nextclade dataset tags and docker images
• Adjusted output parsing to ensure continuity between versions
• Corrected incorrect variable name (gene_annotations_json is now gene_annotations_gff, as described by the Nextclade documentation)

AMRFinderPlus

• Enabled organism-specific AMR gene detection for new organisms: K. pneumoniae, K. oxytoca, K. aerogenes, S. pseudintermedius, Streptococcus pyogenes, V. cholerae, Burkholderia cepacia, Burkholderia pseudomallei, C. coli, C. jejuni, Citrobacter freundii, Clostridioides difficile, Enterobacter cloacae, Enterococcus faecalis, Enterococcus hirae, Enterococcus faecium, Serratia marcescens
• added optional String input expected_taxon to allow the user to override the gambit_predicted_taxon as input for the amrfinderplus task

Shigella characterization

• Added option to change the Shigatyper Docker image
• Updated the default Shigeifinder Docker image

kSNP3

• Added an option to the kSNP3 workflow that allows users to add samples to an existing tree

Freyja

• Updated default docker images
• Changed result when database fails to update in Freyja_FASTQ (now fails instead of succeeding -- thanks @HNHalstead!)

TheiaValidate

• Fixed bug when the validation_criteria_tsv optional input variable was not provided
• Fixed bug when "NA" strings were incorrectly parsed as actual NAs

BaseSpace_Fetch

• Fixed bug when read files contained dots

Snippy/TheiaEuk

• Fixed bug in Snippy gene query task that previously caused product names that include commas to be truncated

What's Changed

• update theiacov GHA tests for v1.0.0 by @rpetit3 in #101
• Updates to nextclade flu dataset tags and image by @jrotieno in #105
• New metadata output on summarize_data task for phylogenetic workflows by @sage-wright in #103
• shigeifinder 1.3.5 updates by @kapsakcj in #109
• TheiaValidate fixes by @sage-wright in #104
• Update task_freyja_one_sample.wdl by @HNHalstead in #116
• BaseSpace_Fetch: convert periods to dashes by @sage-wright in #118
• Update Nextclade Parsing by @sage-wright in #112
• amrfinder & gambit updates by @kapsakcj in #74
• GHA for TheiaCoV_Illumina_PE/_SE by @sage-wright in #119
• Snippy Gene Query fixes by @sage-wright in #102
• Add option to append current kSNP3 run to an existing tree by @cimendes in #122
• Rename variable in nextclade by @sage-wright in #123
• Use docker images stored in Google Artifact Register by @andrewjpage in #120
• small shigella updates, take 2 by @kapsakcj in #125
• update readme by @sage-wright in #128

New Contributors

• @HNHalstead made their first contribution in #116
• @andrewjpage made their first contribution in #120

Full Changelog: v1.0.0...v1.0.1