Changes being added

dev branch

adding the option to run pharokka with --pyrodigal-gv to test for alternate coding genes in config file
sphae plots fix

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. The files are written output.
Updating the QC rule to touch the output file so the error is correctly recorded
the annotate function table after the 3Ps werent being generated, so added that in
add the number of unknown proteins to the final summary file
updated phynteny yaml file to include numpy version
added a python script to the misc folder to merge the RESULTS to one tsv file
adding the total read length to summary file
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

I am updating the default snakemake to v8.11. There have been some changes from v7 to v8, which for now has required me to update

how snakemake can submit jobs to the local cluster - https://snakemake.readthedocs.io/en/v8.4.0/executing/cli.html
The paired end reads have to have the pattern _R1 and _R2 in the sample names, made a note in readme.
Adding documentation on how to add specific number of base pairs to include in the analysis if phage genome length is known by defining the config file handling multiple phages assembled from one sample
Checking for DTRs from checkv results to confirm if the contig is an assembled genome.

added the option to run sphae annotate so assembled genomes or reoriented genomes from dnaapler can be run through only the annotation steps
Cleaning up code, removed use of Attrmap package
Updating the summary file to include phage plot from phynteny output
adding phold results to the summary as needed - making note is phold identified any similar integrase like genes

Updated the annoation steps to Pharokka, Phold and then Phynteny
Also updated the summary file to confirm the presence/absence of specific genes from the annotation outputs
Updated Readme

Sphae can be run on illumina reads and nanopore reads

Quality control - trimnami
Assembly - Megahit for Illumina reads and Flye + Medaka for Nanopore reads Post assembly the reads are run through CheckV, viraverify and looking into graph connection to confirm the genome is assembled
Annotation - Pharokka followed by Phynteny
Generate a summary report file

add another module to map the reads to the assembled genome