V1.2.0 BiG-SCAPE 2, DBCAN, PFAM update

Because of several major changes when updating baclife I recommend reinstalling all conda environments.

Major changes

• We do not longer rely on PROKKA which will no longer be updated. BacLIFE now uses BAKTA for annotation, more proteins will have a description instead of being "hypothetical". BAKTA runs in a seperate Conda enviroment.
• Upgraded to BiG-SCAPE 2, which means MIBiG 4 is now used as a reference database. You now have the option to select which MIBiG version to use. We query the new bigscape2 database directly instead of processing output files.
• In the config file you can now set mibig version and GCF cuttof. Select "Skip" for mibig version to not use any mibig database.
• PFAM, DBCAN have been updated to the latest version
• Better handling when renaming and processing genome names, which should prevent genomes showing up as "NA" in results.

Minor changes

• Manually download eggnog V5 for eggnogmapper as their download functions has been broken for a while
• Make it easier to change ANI threshhold when downloading genomes.
• PCoA color choice in the Shiny app was not always distinguishable or color blind friendly, it can now be customized for some graphs. Handy for generating quick plots.
• All snakmake steps now have defined threads
• Various small fixes and general cleanup of code
• Implemented fixes suggested in #38

v1.1.0

• Updated to Antismash 8.0.4.

To make reruns easier and as preparation for potential nextflow migration/fork:

• Threads for prokka and antismash can be set separately
• Databases are now stored in a separate folder

v1.0.0

bacLIFE v1.0.0