v0.4.0 [Escherichia coli]

Pipeline settings parser and template render have been implemented.

Added

• Config - A class to store all the pipeline configuration
• InternalProcessParamsSet and ExternalProcessParamsSet for loading internal and external process params
• ProcessParams - A class to process and store parameters of pipeline processes
• DataTypes - A class to process and store datatypes
• external.toml to store the list of external pipeline processes
• internal.toml to store the list of internal pipeline processes
• datatypes.toml to store the list of pipeline supported datatypes
• ScriptTemplate - A class for templating nextflow scripts
• ConfigTemplate - A class for templating nextflow config files

Changed

• Simplified the internal and external settings files to contain minimum information
• correlation_table datatype renamed to interaction_table
• Modularize the default settings into separate files - datatypes.toml, internal.toml and external.toml

Fixed

• Filter DeprecationWarning and PendingDeprecationWarning in pytest configuration