v1.5.5

Changes being added

##1.5.5

• phageterm REMOVED, since its breaking things the way I added it. Best, to run this tool separately from the sphae outputs
• phyntney transformer new conda version tested and added
• sphae annotate updates
  • added the option to annotate even fragmented phage contigs,
  • added the feature to provide --proteins as input to sphae annotate instead of --genomes only.
    • These results will not generate genbank files.
    • Annotations generated are in table format
  • Update the summary to include number of contigs, total genome length to summary

v1.5.4

Updates added

• phynteny_transformer updated the yaml file to install and run tool without error
• updating the slurm params in the workflow config and in the rules version
• phageterm added for paired end runs
• updated README

v1.5.3

v1.5.3

• added back --db_dir for sphae install
• fixed issue with fasttree, it should run now with command
  sphae run
• Consistent results to copy the AMR, Defense genes and VFDB genes from phold to the final files

v1.5.2

same as v1.5.1 but trying to get the tool onto pip

v1.5.1

v1.5.1

v1.5.0

updated phynteny to phynteny_transformer
updated medaka to download models with sphae install
updated pharokka yaml file

v1.4.9

updated phynteny to phynteny_transformer

• updated medaka to download models with sphae install
• updated pharokka yaml file

v1.4.8

• db_dir variable error fixed
• moving to using mamba instead of conda as default, and to miniforge instead of miniconda
• updating setup.py to pyproject.toml

v1.4.7

• checkv database error fixed
• Configuring the databases so they can be assigned to user-defined variables, removing the requirement to download or store them within a fixed folder structure

Phylogeny

Added phylogeny in for sphae annotate to build terL and portal gene