Changelogs » Metawibele

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* Added functions for downloading databases
  * Added binary filtering for unsupervised prioritization
  * Added config for interproscan executable file


* 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


* Update different cases for binary filtering
  * Update local and global configuration files
  * Add Rscripts folder


* Update binary filtering approaches for supervised prioritization


* Add


* Add preprocessing workflow
  * Update linear models for association analysis
  * Modify abundance features


* Initial characterization and prioritization processing workflows added