v1.4.5

• catches specific cases of having mutiple circular phages from nanopore assemblies
• updating the code to count the number of hypothetical proteins, and other genes with ambiguous annotations and classifies them as hypothetical
• Addressing issue#36- Phrogs annotated toxin not recognised in sphae summary output, now sphae summary checks for toxins too
• Sphae container added

v1.4.4

Two major changes:

• adding the option to run pharokka with --pyrodigal-gv to test for alternate coding genes. To run the alternative gene prediction tool, change this in the config.yaml file
• The phage plots in the final file were failing. This is fixed now

v1.4.3

Summary file update
- missed adding DTR found or not when only one genome assembled per sample, added this in now
- If recombinases or transposases are found, the genes are written to the summary. Also if AMR, virulence genes, CRSIPR spacers etc are found.
- number of hypothetical proteins
- total read length after QC and subsampling

• Updating the QC rule to touch the output file so the error is correctly recorded
• the annotate function table after the 3Ps weren't being generated, so I added that in
• updated phynteny yaml file to include numpy version
• updating the taxa description in the summary file to include the taxa description, lowest taxa and the isolated host from the pharokka inphared result
• added the --no-polish option for longreads, allows support for the new flowcells and pcbio sequencing

v.1.4.2

v1.4.2

updating readme

V1.4.1

Cleaned up code
updated the summary files
Adding phold and phynteny predicted functions to the summary file

v1.4

Updated the annotation to inlcude phold, updated the summary file and readme

testing pypi workflow

Same as v1.3.3 but testing pypi github workflow

v1.3.3

Just minor updates to checkv yaml file

v1.3.2

Working with python3.12
benchmarks for all the rules added to PROCESSING/benchmarks folder

v1.3.1b

Exactly the same as v1.3.1 - just had to change versions for conda