Metawibele

* Make input/output options available for metawibele on the command line instead of the config file
* Add options for dependent files for each individual step
* Report all DDIs and microbe-human DDIs
* Fixed errors when running DDI-based annotations

* Skip phenotypic association by default
* Skip supervised prioritization if not associating with environmental/phenotypic parameters
* Turn off input/output options in workflows and only use info from the configuration file

* Update DDIs which are supported by PDB
* Update default settings of Maaslin2
* Update function to build dependent databases
* Set cases where running DDIs without domain annotations
* Add bypass modes for each individual domain/motif annotation step
* Rename finalized taxonomic annotation file

* Add utilities to build dependent uniref and domain databases
* Simplify the configurations in metawibele.cfg
* Deprecate sample_list and gene_catalog configs in metawibele.cfg
* Replace 'metawibele_workflow' with 'metawibele'
* Update configuration of depedent databases

* Use UniRef/UniProt databases in HUMAnN
* Remove to map assembled proteins to UniRef50
* Pack default dependent databases: domain databases, taxonomy databases
* Add function to download gloabl and local configuration files
* Remove specific utility scripts in the common folder
* Add option for readling compressed databases
* Balance gridable tasks
* Add option to preprocess outputs from only prokka, only prodigal, or both

* Convert input sources for gridable task
* Reformat annotations of PSORTb, InterProScan
* Add EffectiveT3 to predict effector (TBD)
* Make config file for MSPminer as optional