4.15.25245

Minor update:

• Update bakta to 1.11.3-6.0-light
• Update multiqc to 1.30
• Update datasets to 18.5.0

4.15.25218

Moderate update that may impact some users. Although we went through a few dozen tests, we're still worried these changes may impact users. We recommend creating an issue if/when one arises.

Moderate updates:

• Removed all ENV output channels. These differ in how they are treated between nextflow versions. The ENV channels worked for for nextflow version 25.04.6, but not nextflow versions 23* or prior (which some cloud systems use as well as local partners). In order to reduce our complaints, we removed all the ENV output channels and replaced them with other functions.
• There is a new param: min_core_per . Instead of looking at the number of genes in the core genome, this looks at the percentage of genes that are part of the core genome. The default is 0.5 (i.e. 50% of each sample's genes need to be part of the core genome to proceed). The phylogenetic subworkflow is intended to be used for clonal expansions, for which we recommend at least 70% of the genes of organism are part of the core genome.
• The default for min_core_genes is reduced to 500.

Minor updates:

• update amrfinderplus to 4.0.23-2025-07-16.1
• update blast to 2.17.0
• update fastp to 1.0.1
• update kaptive to 3.1.0
• update pandas to 2.3.0
• update kraken2 to 2.1.6

4.9.25175

• Update bakta to 1.11.0-6.0-light
• Update multiqc to 1.28
• Update amrfinderplus to 4.0.23-2025-06-03.1
• Update datasets to 18.0.2
• Update panaroo to 1.5.2
• Update spades to 4.2.0

v4.9.25127

Minor release to update components

• Update elgato to 1.21.2
• Update fastp to 0.24.1
• Update kraken2 to 2.1.5
• Update multiqc to 1.28
• Update amrfinderplus to 4.0.22-2025-03-25.1

4.9.25098

Minor release:

• update ncbi-amrfinderplus to 4.0.19-2024-12-18.1
• update bakta to 1.10.4-5.1-light
• update datasets to 16.41.0
• update el gato to 1.21.0
• update iqtree2 to 2.4.0
• update kleborate to 3.1.3
• update mlst to 2.23.0-2024-12-31 (see StaPH-B/docker-builds#1169 for more information)
• update multiqc to 1.27.1
• update plasmidfinder to 2.1.6_2025-02-19
• update spades to 4.1.0

4.9.25035

Actual release:

Update bakta to 1.10.3-5.1-light
Update elgato to 1.20.2
Update fastp to 0.24.0
Update mlst to 2.23.0-2025-02-01
Update amrfinderplus to 4.0.15-2024-12-18.1
Update datasets to 16.38.1
Update panaroo to 1.5.1

4.9.24345

Pre-release with some moderate changes:

• bakta has replaced prokka for genome annotation
  • prokka can still be used by setting params.annotator = prokka
• bbduk has been removed (phix removal doesn't seem to be needed with modern sequencers)
• satisfies vs code nextflow linter (version 1.0.4)
  • includes moving all publishDir to conf/modules.config
• adds meningotype
• updates usage for kleborate (may change serotyping)
• updates usage for kaptive (may change serotyping)
• minor updates to other steps
• moves more processes to dockerhub

4.5.24310

Minor release:

• Update mlst to 2.23.0-2024-11-01
• Update blast to 2.16.0
• Update elgato to 1.20.1
• Update iqtree2 to 2.3.6
• Update datasets to 16.30.0
• Update pbptyper to 2.0.0

4.5.24276

Minor release:

Updates mlst to 2.23.0-2024-10-01

4.5.24250

Minor update

• Update amrfinder to 3.12.8-2024-07-22.1
• Update elgato to 1.19.0
• Update mlst to 2.23.0-2024-09-01