3.4.20230919

Moderate update - but may come as a great relief to some:

• current-datasets is now set to false by default - this should resolve a lot of issues with connectivity
• changed datasets download to only download new genomes (does not download genomes from list)
  • This retires params.genome_references
• updated fastani to 1.34
• since fastani now allows *.gz as input, the included genomes are now separate compressed files
  • the 'decompression' process was removed
• changed params.fastani_ref to accept a comma-delimited list of fasta files (or fasta.gz files) to be added to the fastani references
• added params.fastani_ref_list to accept a file with a on each line for fasta files (or fasta.gz files) to be added to the fastani references

3.3.20230815

Minor release:

• updated amrfinderplus to 3.11.18-2023-08-08.2

3.3.20230808

Moderate release:

• added to test cases
• adjusted GA test
• removed kraken2 running on contigs (long story - but in essence this is out of kraken2's normal use and someone got some results they were not expecting and took them too seriously)
• updated amrfinderplus to 3.11.17-2023-07-13.2

3.2.20230803

Minor updates that are "behind the scenes"

• adds python script for common file manipulations
• adds python script for datasets accessions
• uses new UPHL-maintained container for datasets (for python 3)
• removed genome length from SNP matrix file

3.2.20230718

Minor update

• shigatyper has been updated to 2.0.5
• mlst has been updated to 2.23.0-2023-07
• fixed bug when quast doesn't create file
• adjusted HeatCluster.py to allow for all snp-dists output (-b and -c, -m will cause the script to exit).

3.2.20230711 - 2

A few bug fixes, as well as contributions from @DrB-S

3.2.20230711

Included in this update

• update iqtree2 to version 2.1.3
• update amrfinderplus to version 3.11.14-2023-04-17.1
• update kraken2 to version 2.1.3

Other updates

• move from biocontainers/pandas to uphl/seaborn
• add heatmap figure for SNP matrices

• add QC metrics during SNP dists

Fix bugs

• amrfinder is now alphabetized on gene name for summary file
• changed datasets genomes file to include wildcard to avoid special character

3.2.20230620

Minor bug fix

3.2.20230613

MINOR UPDATE

• updates container for
  • blast to 2.14.0
  • fastp to 0.23.4
  • datasets to 15.2.0
• has a workaround for datasets timeouts
• allows more matches from NCBI datasets for those without representative genomes
  • removes MAG matches
• bug fix for samples without fastani matches

3.2.20230523

Mostly minor changes internally, but

• changed summary file (again)
• removed fastqscan
• added additional ways to determine size
• added warnings
• added a clear coverage column to the sample sheet
  • added coverage for hypothetical genome sizes in extended sample sheet
• fixed error if there's no matches in fastani